Starting phenix.real_space_refine on Wed May 28 13:20:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.map" model { file = "/net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y89_39038/05_2025/8y89_39038.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 19521 2.51 5 N 5015 2.21 5 O 5934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 1.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30645 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 8482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1094, 8482 Classifications: {'peptide': 1094} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1048} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 9126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9126 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 149 Chain: "B" Number of atoms: 9116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9116 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1137} Chain breaks: 2 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 132 Chain: "T" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1702 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1718 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 14, 'TRANS': 222} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 122 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 89 Chain: "D" 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: "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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 18.87, per 1000 atoms: 0.62 Number of scatterers: 30645 At special positions: 0 Unit cell: (156.62, 143.5, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 5934 8.00 N 5015 7.00 C 19521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=64, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 485 " - pdb=" SG CYS C 516 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS T 410 " - pdb=" SG CYS T 426 " distance=2.03 Simple disulfide: pdb=" SG CYS T 437 " - pdb=" SG CYS T 465 " distance=2.03 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 437 " - pdb=" SG CYS G 465 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A1301 " - " ASN A 192 " " NAG A1302 " - " ASN A 703 " " NAG A1303 " - " ASN A 793 " " NAG A1304 " - " ASN A1211 " " NAG B1301 " - " ASN B 355 " " NAG B1302 " - " ASN B 924 " " NAG B1303 " - " ASN B 725 " " NAG B1304 " - " ASN B1211 " " NAG B1305 " - " ASN B 58 " " NAG C1301 " - " ASN C 771 " " NAG C1302 " - " ASN C 793 " " NAG C1303 " - " ASN C 924 " " NAG C1304 " - " ASN C1211 " " NAG D 1 " - " ASN A 132 " " NAG E 1 " - " ASN A 188 " " NAG F 1 " - " ASN A 664 " " NAG H 1 " - " ASN A 725 " " NAG I 1 " - " ASN A 58 " " NAG J 1 " - " ASN C 58 " " NAG K 1 " - " ASN C 664 " " NAG L 1 " - " ASN C 725 " " NAG M 1 " - " ASN B 192 " " NAG N 1 " - " ASN B 664 " " NAG O 1 " - " ASN B 793 " Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 4.6 seconds 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7420 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 72 sheets defined 22.6% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.02 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.516A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.535A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.927A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.602A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.820A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 704 removed outlier: 3.537A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 830 Processing helix chain 'A' and resid 832 through 862 removed outlier: 3.896A pdb=" N CYS A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.867A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.846A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 4.116A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.528A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.795A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1019 removed outlier: 3.607A pdb=" N ASN A1009 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1046 removed outlier: 3.716A pdb=" N GLN A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1058 through 1063 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.562A pdb=" N ALA A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.685A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.615A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.702A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 removed outlier: 3.612A pdb=" N CYS C 556 " --> pdb=" O GLU C 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 701 Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.644A pdb=" N VAL C 818 " --> pdb=" O CYS C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.695A pdb=" N HIS C 826 " --> pdb=" O TYR C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 833 No H-bonds generated for 'chain 'C' and resid 831 through 833' Processing helix chain 'C' and resid 835 through 862 removed outlier: 4.133A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 841 " --> pdb=" O ASP C 837 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 843 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 3.688A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.532A pdb=" N ASN C 941 " --> pdb=" O VAL C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.576A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.728A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.664A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.738A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.807A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1063 Processing helix chain 'C' and resid 1064 through 1065 No H-bonds generated for 'chain 'C' and resid 1064 through 1065' Processing helix chain 'C' and resid 1066 through 1069 Processing helix chain 'C' and resid 1070 through 1114 removed outlier: 3.817A pdb=" N ILE C1074 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.215A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.685A pdb=" N PHE B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.571A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 445 through 449 removed outlier: 3.601A pdb=" N TYR B 448 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 445 through 449' Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.574A pdb=" N ASN B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.581A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 813 through 818 removed outlier: 3.704A pdb=" N PHE B 817 " --> pdb=" O ASP B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 836 through 862 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.637A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 923 removed outlier: 3.892A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 928 removed outlier: 4.084A pdb=" N GLY B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 928 " --> pdb=" O ASN B 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 928' Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 951 through 966 removed outlier: 4.013A pdb=" N ALA B 966 " --> pdb=" O ALA B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 998 removed outlier: 3.801A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1018 Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.558A pdb=" N ALA B1027 " --> pdb=" O PRO B1023 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.737A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.576A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.664A pdb=" N ALA B1070 " --> pdb=" O ASP B1066 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'T' and resid 299 through 303 Processing helix chain 'T' and resid 406 through 411 Processing helix chain 'T' and resid 480 through 490 Processing helix chain 'G' and resid 299 through 303 Processing helix chain 'G' and resid 304 through 307 Processing helix chain 'G' and resid 406 through 411 Processing helix chain 'G' and resid 480 through 492 removed outlier: 3.614A pdb=" N GLY G 492 " --> pdb=" O MET G 488 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 4.139A pdb=" N ARG A 34 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 76 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 75 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.366A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS B 665 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 317 " --> pdb=" O ASP B 623 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 4.972A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.819A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 113 removed outlier: 4.147A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 183 through 190 removed outlier: 3.946A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS A 151 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.796A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 317 removed outlier: 3.634A pdb=" N TYR A 622 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB2, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.603A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 365 through 371 removed outlier: 6.183A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 459 through 462 Processing sheet with id=AB5, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.686A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 648 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.688A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.138A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 786 through 795 removed outlier: 6.936A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 798 through 803 removed outlier: 3.791A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 809 through 811 removed outlier: 4.232A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC3, first strand: chain 'A' and resid 1162 through 1163 Processing sheet with id=AC4, first strand: chain 'A' and resid 1169 through 1172 removed outlier: 4.067A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC6, first strand: chain 'C' and resid 35 through 39 removed outlier: 4.713A pdb=" N PHE C 74 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 61 through 67 removed outlier: 3.641A pdb=" N LEU C 61 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 80 through 81 removed outlier: 8.014A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 221 through 227 removed outlier: 5.647A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 211 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 110 through 113 Processing sheet with id=AD2, first strand: chain 'C' and resid 183 through 190 removed outlier: 6.592A pdb=" N ALA C 150 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C 186 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 148 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN C 188 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 146 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 302 through 307 removed outlier: 3.770A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.766A pdb=" N ARG C 319 " --> pdb=" O ASP C 623 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'C' and resid 346 through 349 removed outlier: 6.565A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 346 through 349 Processing sheet with id=AD8, first strand: chain 'C' and resid 353 through 354 removed outlier: 4.203A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AE1, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.353A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AE3, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AE4, first strand: chain 'C' and resid 632 through 635 Processing sheet with id=AE5, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.183A pdb=" N ASN C 725 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 764 " --> pdb=" O ASN C 725 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR C 766 " --> pdb=" O THR C 727 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR C 729 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.094A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.697A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY C1140 " --> pdb=" O ASN C1136 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN C1136 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C1142 " --> pdb=" O VAL C1134 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C1134 " --> pdb=" O LEU C1142 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C1144 " --> pdb=" O SER C1132 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER C1132 " --> pdb=" O ILE C1144 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE C1146 " --> pdb=" O ILE C1130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.114A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.939A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1175 through 1179 Processing sheet with id=AF2, first strand: chain 'B' and resid 62 through 67 removed outlier: 3.671A pdb=" N LEU B 267 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.618A pdb=" N TYR B 203 " --> pdb=" O TYR B 210 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 211 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 96 through 97 removed outlier: 4.412A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 136 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 109 through 113 Processing sheet with id=AF6, first strand: chain 'B' and resid 155 through 160 removed outlier: 11.050A pdb=" N TYR B 158 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N HIS B 175 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B 160 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 302 through 306 removed outlier: 3.506A pdb=" N LEU B 690 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 713 " --> pdb=" O VAL B 720 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF9, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.398A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AG2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AG3, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AG4, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AG5, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AG6, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.655A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 786 through 795 removed outlier: 6.648A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 798 through 804 removed outlier: 3.602A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.089A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 1162 through 1163 Processing sheet with id=AH2, first strand: chain 'B' and resid 1169 through 1172 Processing sheet with id=AH3, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AH4, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.350A pdb=" N ASN T 398 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 383 " --> pdb=" O ASN T 398 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'T' and resid 260 through 261 removed outlier: 4.465A pdb=" N CYS T 426 " --> pdb=" O ILE T 405 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 278 through 281 removed outlier: 5.303A pdb=" N HIS T 279 " --> pdb=" O VAL T 275 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL T 275 " --> pdb=" O HIS T 279 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS T 281 " --> pdb=" O LEU T 273 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR T 326 " --> pdb=" O ALA T 310 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS T 350 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL T 331 " --> pdb=" O LEU T 348 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU T 348 " --> pdb=" O VAL T 331 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'T' and resid 446 through 449 Processing sheet with id=AH8, first strand: chain 'G' and resid 260 through 261 removed outlier: 4.457A pdb=" N ASN G 398 " --> pdb=" O GLY G 383 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY G 383 " --> pdb=" O ASN G 398 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU G 378 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N SER G 448 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP G 380 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL G 446 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER G 382 " --> pdb=" O PRO G 444 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY G 457 " --> pdb=" O PRO G 444 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 446 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU G 455 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER G 448 " --> pdb=" O TRP G 453 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TRP G 453 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER G 460 " --> pdb=" O VAL G 473 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL G 473 " --> pdb=" O SER G 460 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 278 through 281 removed outlier: 5.333A pdb=" N HIS G 279 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL G 275 " --> pdb=" O HIS G 279 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS G 281 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 326 " --> pdb=" O ALA G 310 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS G 350 " --> pdb=" O GLU G 329 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL G 331 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU G 348 " --> pdb=" O VAL G 331 " (cutoff:3.500A) 1019 hydrogen bonds defined for protein. 2772 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: 14.15 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9773 1.34 - 1.46: 7876 1.46 - 1.58: 13519 1.58 - 1.70: 0 1.70 - 1.82: 207 Bond restraints: 31375 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 31370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 41771 1.23 - 2.45: 808 2.45 - 3.68: 207 3.68 - 4.91: 14 4.91 - 6.13: 11 Bond angle restraints: 42811 Sorted by residual: angle pdb=" C ALA A 244 " pdb=" N ILE A 245 " pdb=" CA ILE A 245 " ideal model delta sigma weight residual 121.97 126.46 -4.49 1.80e+00 3.09e-01 6.23e+00 angle pdb=" N VAL A 131 " pdb=" CA VAL A 131 " pdb=" C VAL A 131 " ideal model delta sigma weight residual 110.30 107.92 2.38 9.70e-01 1.06e+00 6.04e+00 angle pdb=" N GLY C 653 " pdb=" CA GLY C 653 " pdb=" C GLY C 653 " ideal model delta sigma weight residual 113.18 118.35 -5.17 2.37e+00 1.78e-01 4.76e+00 angle pdb=" N PRO B1067 " pdb=" CA PRO B1067 " pdb=" C PRO B1067 " ideal model delta sigma weight residual 110.70 113.22 -2.52 1.22e+00 6.72e-01 4.28e+00 angle pdb=" N SER A 820 " pdb=" CA SER A 820 " pdb=" C SER A 820 " ideal model delta sigma weight residual 111.02 113.54 -2.52 1.22e+00 6.72e-01 4.28e+00 ... (remaining 42806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 18663 21.76 - 43.51: 359 43.51 - 65.27: 26 65.27 - 87.02: 7 87.02 - 108.78: 4 Dihedral angle restraints: 19059 sinusoidal: 7511 harmonic: 11548 Sorted by residual: dihedral pdb=" CA ASN A 243 " pdb=" C ASN A 243 " pdb=" N ALA A 244 " pdb=" CA ALA A 244 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" SG CYS C 151 " pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" CA CYS C 183 " ideal model delta sinusoidal sigma weight residual -73.00 -4.79 -68.21 1 2.00e+01 2.50e-03 1.51e+01 dihedral pdb=" O4 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C5 BMA O 3 " pdb=" O5 BMA O 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.93 108.78 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 19056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4162 0.054 - 0.108: 711 0.108 - 0.162: 94 0.162 - 0.216: 0 0.216 - 0.270: 1 Chirality restraints: 4968 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE C 812 " pdb=" N ILE C 812 " pdb=" C ILE C 812 " pdb=" CB ILE C 812 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" C2 BMA O 3 " pdb=" C1 BMA O 3 " pdb=" C3 BMA O 3 " pdb=" O2 BMA O 3 " both_signs ideal model delta sigma weight residual False 2.47 2.61 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 4965 not shown) Planarity restraints: 5501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A1067 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B1067 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C1067 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " 0.021 5.00e-02 4.00e+02 ... (remaining 5498 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2640 2.75 - 3.29: 29284 3.29 - 3.82: 47902 3.82 - 4.36: 54013 4.36 - 4.90: 96695 Nonbonded interactions: 230534 Sorted by model distance: nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.210 3.040 nonbonded pdb=" O LYS C 377 " pdb=" OG SER C 381 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR B 832 " pdb=" OD1 ASP B1075 " model vdw 2.246 3.040 nonbonded pdb=" O LYS A 377 " pdb=" OG SER A 381 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 715 " pdb=" O GLY B 718 " model vdw 2.271 3.040 ... (remaining 230529 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 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 89 or (resid 90 and (name N or nam \ e CA or name C or name O or name CB )) or resid 91 or (resid 92 and (name N or n \ ame CA or name C or name O or name CB )) or resid 93 or (resid 94 through 96 and \ (name N or name CA or name C or name O or name CB )) or resid 97 through 104 or \ (resid 105 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 6 through 110 or (resid 111 through 112 and (name N or name CA or name C or name \ O or name CB )) or resid 113 or (resid 114 through 115 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 122 or (resid 123 and (nam \ e N or name CA or name C or name O or name CB )) or resid 124 through 128 or (re \ sid 129 through 131 and (name N or name CA or name C or name O or name CB )) or \ resid 132 through 159 or (resid 160 through 166 and (name N or name CA or name C \ or name O or name CB )) or resid 167 through 169 or (resid 170 through 172 and \ (name N or name CA or name C or name O or name CB )) or resid 173 through 181 or \ (resid 182 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 3 through 195 or (resid 196 and (name N or name CA or name C or name O or name C \ B )) or resid 197 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 231 or (resid 232 through 236 and (nam \ e N or name CA or name C or name O or name CB )) or resid 237 or (resid 238 and \ (name N or name CA or name C or name O or name CB )) or resid 239 through 241 or \ (resid 242 through 245 and (name N or name CA or name C or name O or name CB )) \ or resid 246 through 249 or (resid 250 through 252 and (name N or name CA or na \ me C or name O or name CB )) or resid 253 through 352 or (resid 353 and (name N \ or name CA or name C or name O or name CB )) or resid 354 through 360 or (resid \ 361 and (name N or name CA or name C or name O or name CB )) or resid 362 throug \ h 363 or (resid 364 and (name N or name CA or name C or name O or name CB )) or \ resid 365 through 372 or (resid 373 and (name N or name CA or name C or name O o \ r name CB )) or resid 374 through 376 or (resid 377 and (name N or name CA or na \ me C or name O or name CB )) or resid 378 or (resid 379 and (name N or name CA o \ r name C or name O or name CB )) or resid 380 or (resid 381 through 384 and (nam \ e N or name CA or name C or name O or name CB )) or resid 385 through 407 or (re \ sid 408 and (name N or name CA or name C or name O or name CB )) or resid 409 th \ rough 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 464 or (resid 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 through 592 or (resid 593 through 595 and (name N \ or name CA or name C or name O or name CB )) or resid 596 or (resid 597 through \ 599 and (name N or name CA or name C or name O or name CB )) or resid 600 throug \ h 602 or (resid 603 and (name N or name CA or name C or name O or name CB )) or \ resid 604 through 615 or (resid 616 and (name N or name CA or name C or name O o \ r name CB )) or resid 617 through 619 or (resid 620 and (name N or name CA or na \ me C or name O or name CB )) or resid 621 through 626 or (resid 627 and (name N \ or name CA or name C or name O or name CB )) or resid 628 through 633 or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throug \ h 651 or (resid 652 and (name N or name CA or name C or name O or name CB )) or \ resid 653 or (resid 654 and (name N or name CA or name C or name O or name CB )) \ or resid 655 through 665 or (resid 666 and (name N or name CA or name C or name \ O or name CB )) or resid 667 through 708 or (resid 709 and (name N or name CA o \ r name C or name O or name CB )) or resid 710 through 744 or (resid 745 and (nam \ e N or name CA or name C or name O or name CB )) or resid 746 through 779 or (re \ sid 780 and (name N or name CA or name C or name O or name CB )) or resid 781 th \ rough 836 or (resid 837 and (name N or name CA or name C or name O or name CB )) \ or resid 838 through 929 or (resid 930 through 932 and (name N or name CA or na \ me C or name O or name CB )) or resid 933 through 998 or (resid 999 and (name N \ or name CA or name C or name O or name CB )) or resid 1000 through 1065 or (resi \ d 1066 and (name N or name CA or name C or name O or name CB )) or resid 1067 th \ rough 1148 or (resid 1149 and (name N or name CA or name C or name O or name CB \ )) or resid 1150 through 1181 or (resid 1182 through 1183 and (name N or name CA \ or name C or name O or name CB )) or resid 1184 through 1199 or (resid 1200 and \ (name N or name CA or name C or name O or name CB )) or resid 1201 through 1216 \ or (resid 1217 and (name N or name CA or name C or name O or name CB )) or resi \ d 1218 through 1221 or resid 1301 through 1304)) selection = (chain 'B' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 24 or (resid 25 through 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 29 or resid 32 through 84 or (res \ id 85 through 87 and (name N or name CA or name C or name O or name CB )) or res \ id 88 through 89 or (resid 90 and (name N or name CA or name C or name O or name \ CB )) or resid 91 or (resid 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 or (resid 94 through 96 and (name N or name CA or name C or \ name O or name CB )) or resid 97 through 104 or (resid 105 and (name N or name \ CA or name C or name O or name CB )) or resid 106 through 110 or (resid 111 thro \ ugh 112 and (name N or name CA or name C or name O or name CB )) or resid 113 or \ (resid 114 through 115 and (name N or name CA or name C or name O or name CB )) \ or resid 116 through 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 129 or (resid 130 through 131 and (name N \ or name CA or name C or name O or name CB )) or resid 132 or (resid 133 and (nam \ e N or name CA or name C or name O or name CB )) or resid 134 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 156 or (resid 157 through 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 or (resid 160 through 166 and (name N or name CA o \ r name C or name O or name CB )) or resid 167 through 168 or (resid 169 through \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throug \ h 204 or (resid 205 through 206 and (name N or name CA or name C or name O or na \ me CB )) or resid 207 through 237 or (resid 238 and (name N or name CA or name C \ or name O or name CB )) or resid 239 through 241 or (resid 242 through 245 and \ (name N or name CA or name C or name O or name CB )) or resid 246 through 249 or \ (resid 250 through 252 and (name N or name CA or name C or name O or name CB )) \ or resid 253 through 288 or (resid 289 and (name N or name CA or name C or name \ O or name CB )) or resid 290 through 308 or resid 313 through 323 or resid 326 \ through 352 or (resid 353 and (name N or name CA or name C or name O or name CB \ )) or resid 354 through 407 or (resid 408 and (name N or name CA or name C or na \ me O or name CB )) or resid 409 through 412 or (resid 413 and (name N or name CA \ or name C or name O or name CB )) or resid 414 through 464 or (resid 465 and (n \ ame N or name CA or name C or name O or name CB )) or resid 466 through 468 or r \ esid 536 through 550 or resid 572 through 606 or (resid 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 626 or (resid 627 and \ (name N or name CA or name C or name O or name CB )) or resid 628 through 708 or \ (resid 709 and (name N or name CA or name C or name O or name CB )) or resid 71 \ 0 through 744 or (resid 745 and (name N or name CA or name C or name O or name C \ B )) or resid 746 through 779 or (resid 780 and (name N or name CA or name C or \ name O or name CB )) or resid 781 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB )) or resid 808 through 890 or (resid 891 and \ (name N or name CA or name C or name O or name CB )) or resid 899 through 998 or \ (resid 999 and (name N or name CA or name C or name O or name CB )) or resid 10 \ 00 through 1199 or (resid 1200 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1201 through 1221 or resid 1301 through 1304)) selection = (chain 'C' and ((resid 14 and (name N or name CA or name C or name O or name CB \ )) or resid 15 through 24 or (resid 25 through 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 29 or resid 32 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 84 or (resid 85 through 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 128 or (resid 129 through 131 and (name N or name CA \ or name C or name O or name CB )) or resid 132 or (resid 133 and (name N or name \ CA or name C or name O or name CB )) or resid 134 through 146 or (resid 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 through 154 o \ r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 56 or (resid 157 through 158 and (name N or name CA or name C or name O or name \ CB )) or resid 159 through 160 or (resid 161 through 166 and (name N or name CA \ or name C or name O or name CB )) or resid 167 through 168 or (resid 169 through \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throu \ gh 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) or \ resid 183 through 195 or (resid 196 and (name N or name CA or name C or name O \ or name CB )) or resid 197 through 217 or (resid 218 and (name N or name CA or n \ ame C or name O or name CB )) or resid 219 through 231 or (resid 232 through 236 \ and (name N or name CA or name C or name O or name CB )) or resid 237 through 2 \ 44 or (resid 245 and (name N or name CA or name C or name O or name CB )) or res \ id 246 through 288 or (resid 289 and (name N or name CA or name C or name O or n \ ame CB )) or resid 290 through 308 or resid 313 through 323 or resid 326 through \ 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or r \ esid 362 through 363 or (resid 364 and (name N or name CA or name C or name O or \ name CB )) or resid 365 through 372 or (resid 373 and (name N or name CA or nam \ e C or name O or name CB )) or resid 374 through 376 or (resid 377 and (name N o \ r name CA or name C or name O or name CB )) or resid 378 or (resid 379 and (name \ N or name CA or name C or name O or name CB )) or resid 380 or (resid 381 throu \ gh 384 and (name N or name CA or name C or name O or name CB )) or resid 385 thr \ ough 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) \ or resid 414 through 444 or (resid 445 and (name N or name CA or name C or name \ O or name CB )) or resid 446 through 468 or resid 536 through 550 or resid 572 t \ hrough 592 or (resid 593 through 595 and (name N or name CA or name C or name O \ or name CB )) or resid 596 or (resid 597 through 599 and (name N or name CA or n \ ame C or name O or name CB )) or resid 600 through 602 or (resid 603 and (name N \ or name CA or name C or name O or name CB )) or resid 604 through 606 or resid \ 609 through 615 or (resid 616 and (name N or name CA or name C or name O or name \ CB )) or resid 617 through 619 or (resid 620 and (name N or name CA or name C o \ r name O or name CB )) or resid 621 through 631 or (resid 632 and (name N or nam \ e CA or name C or name O or name CB )) or resid 633 or (resid 634 and (name N or \ name CA or name C or name O or name CB )) or resid 635 through 651 or (resid 65 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 653 or (resi \ d 654 and (name N or name CA or name C or name O or name CB )) or resid 655 thro \ ugh 665 or (resid 666 and (name N or name CA or name C or name O or name CB )) o \ r resid 667 through 806 or (resid 807 and (name N or name CA or name C or name O \ or name CB )) or resid 808 through 890 or (resid 891 and (name N or name CA or \ name C or name O or name CB )) or resid 899 through 930 or (resid 931 through 93 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 933 through \ 1065 or (resid 1066 and (name N or name CA or name C or name O or name CB )) or \ resid 1067 through 1148 or (resid 1149 and (name N or name CA or name C or name \ O or name CB )) or resid 1150 through 1181 or (resid 1182 through 1183 and (name \ N or name CA or name C or name O or name CB )) or resid 1184 through 1216 or (r \ esid 1217 and (name N or name CA or name C or name O or name CB )) or resid 1218 \ through 1221 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'G' and (resid 256 through 370 or (resid 371 through 373 and (name N or n \ ame CA or name C or name O or name CB )) or resid 374 through 424 or (resid 425 \ and (name N or name CA or name C or name O or name CB )) or resid 426 through 47 \ 5 or (resid 476 through 480 and (name N or name CA or name C or name O or name C \ B )) or resid 481 through 492)) selection = (chain 'T' and (resid 256 through 460 or (resid 461 and (name N or name CA or na \ me C or name O or name CB )) or resid 462 through 492)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 72.630 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.002 0.040 31475 Z= 0.113 Angle : 0.438 6.132 43047 Z= 0.227 Chirality : 0.041 0.270 4968 Planarity : 0.003 0.047 5477 Dihedral : 7.937 108.776 11447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.78 % Allowed : 4.78 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.12), residues: 3922 helix: 0.36 (0.19), residues: 735 sheet: -0.74 (0.17), residues: 815 loop : -2.58 (0.11), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 344 HIS 0.003 0.000 HIS A 142 PHE 0.008 0.001 PHE C 200 TYR 0.010 0.001 TYR C1148 ARG 0.002 0.000 ARG C 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 24) link_NAG-ASN : angle 0.95198 ( 72) link_BETA1-4 : bond 0.00335 ( 12) link_BETA1-4 : angle 0.82030 ( 36) hydrogen bonds : bond 0.14284 ( 998) hydrogen bonds : angle 5.17686 ( 2772) SS BOND : bond 0.00106 ( 64) SS BOND : angle 0.56672 ( 128) covalent geometry : bond 0.00227 (31375) covalent geometry : angle 0.43540 (42811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 661 time to evaluate : 3.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.8252 (t80) cc_final: 0.7848 (t80) REVERT: A 182 LEU cc_start: 0.8249 (pt) cc_final: 0.7729 (pt) REVERT: A 318 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.5229 (t80) REVERT: A 625 TYR cc_start: 0.7706 (m-80) cc_final: 0.7283 (m-80) REVERT: A 1045 GLN cc_start: 0.8147 (tp40) cc_final: 0.7932 (tp40) REVERT: A 1049 ASN cc_start: 0.8294 (m-40) cc_final: 0.7975 (m-40) REVERT: C 258 VAL cc_start: 0.7887 (m) cc_final: 0.7660 (p) REVERT: C 280 VAL cc_start: 0.8179 (m) cc_final: 0.7924 (p) REVERT: C 878 ASP cc_start: 0.7413 (p0) cc_final: 0.7114 (p0) REVERT: C 885 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8125 (ptmm) REVERT: C 906 LEU cc_start: 0.8230 (mp) cc_final: 0.7917 (mp) REVERT: C 1000 ASN cc_start: 0.8056 (m110) cc_final: 0.7819 (m110) REVERT: C 1095 ASP cc_start: 0.7292 (t0) cc_final: 0.6955 (t0) REVERT: C 1096 ILE cc_start: 0.8616 (tp) cc_final: 0.8408 (tp) REVERT: C 1202 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7381 (t) REVERT: B 139 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 164 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7805 (mmmt) REVERT: B 261 LEU cc_start: 0.8433 (mt) cc_final: 0.8205 (mp) REVERT: B 320 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7147 (ttm-80) REVERT: B 722 ASN cc_start: 0.7842 (t0) cc_final: 0.7214 (t0) REVERT: B 732 SER cc_start: 0.8597 (p) cc_final: 0.8344 (m) REVERT: B 813 ASP cc_start: 0.7362 (t0) cc_final: 0.7144 (t0) REVERT: B 825 CYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5264 (t) REVERT: B 865 VAL cc_start: 0.8074 (t) cc_final: 0.7783 (p) REVERT: B 866 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (p) REVERT: B 999 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7729 (mtpp) REVERT: B 1010 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7860 (ttmm) REVERT: B 1048 PHE cc_start: 0.8561 (m-10) cc_final: 0.8056 (m-80) REVERT: B 1164 LEU cc_start: 0.8452 (mm) cc_final: 0.8144 (mp) REVERT: B 1174 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7411 (mm-40) REVERT: B 1185 MET cc_start: 0.7059 (mtm) cc_final: 0.6447 (mtm) REVERT: B 1198 SER cc_start: 0.8391 (p) cc_final: 0.8181 (t) REVERT: B 1214 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7587 (mtpp) REVERT: T 488 MET cc_start: -0.1073 (mmm) cc_final: -0.1483 (mtm) REVERT: G 355 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5450 (mt) outliers start: 59 outliers final: 12 residues processed: 707 average time/residue: 0.3917 time to fit residues: 442.8058 Evaluate side-chains 557 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 539 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1202 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 825 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 1.9990 chunk 297 optimal weight: 0.6980 chunk 165 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 308 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 187 optimal weight: 0.0870 chunk 229 optimal weight: 6.9990 chunk 356 optimal weight: 9.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 591 ASN A 605 ASN A 709 GLN A 847 ASN A 863 GLN A1046 GLN C 26 ASN C 99 ASN C 140 GLN C 142 HIS C 188 ASN C 331 ASN C 445 ASN C 591 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 GLN C 870 ASN C 881 ASN C1016 GLN C1038 GLN C1041 ASN C1059 GLN B 142 HIS B 188 ASN B 410 GLN B 863 GLN B 988 ASN B1079 ASN B1135 GLN T 276 GLN G 276 GLN ** G 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.190558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140561 restraints weight = 53123.601| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.00 r_work: 0.3502 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 31475 Z= 0.139 Angle : 0.532 19.512 43047 Z= 0.271 Chirality : 0.044 0.272 4968 Planarity : 0.004 0.049 5477 Dihedral : 5.066 58.767 5003 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.36 % Allowed : 9.65 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.13), residues: 3922 helix: 1.26 (0.20), residues: 767 sheet: -0.38 (0.17), residues: 808 loop : -2.26 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 644 HIS 0.008 0.001 HIS C1145 PHE 0.027 0.001 PHE A 222 TYR 0.027 0.001 TYR B 649 ARG 0.008 0.000 ARG A 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 24) link_NAG-ASN : angle 3.13608 ( 72) link_BETA1-4 : bond 0.00533 ( 12) link_BETA1-4 : angle 1.65811 ( 36) hydrogen bonds : bond 0.04156 ( 998) hydrogen bonds : angle 4.45937 ( 2772) SS BOND : bond 0.00316 ( 64) SS BOND : angle 1.34490 ( 128) covalent geometry : bond 0.00319 (31375) covalent geometry : angle 0.50972 (42811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 576 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.8445 (t80) cc_final: 0.8139 (t80) REVERT: A 102 ILE cc_start: 0.8425 (mm) cc_final: 0.8139 (mm) REVERT: A 186 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8365 (ttpt) REVERT: A 221 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 264 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7703 (mtm-85) REVERT: A 625 TYR cc_start: 0.7786 (m-80) cc_final: 0.6816 (m-80) REVERT: A 730 SER cc_start: 0.8506 (t) cc_final: 0.8266 (m) REVERT: A 1048 PHE cc_start: 0.8585 (m-10) cc_final: 0.8341 (m-80) REVERT: A 1049 ASN cc_start: 0.8529 (m-40) cc_final: 0.8251 (m-40) REVERT: A 1059 GLN cc_start: 0.8533 (tp40) cc_final: 0.8226 (tp-100) REVERT: C 258 VAL cc_start: 0.8006 (m) cc_final: 0.7762 (p) REVERT: C 280 VAL cc_start: 0.8422 (m) cc_final: 0.8180 (p) REVERT: C 623 ASP cc_start: 0.8120 (t0) cc_final: 0.7870 (t0) REVERT: C 666 THR cc_start: 0.8323 (p) cc_final: 0.8074 (p) REVERT: C 763 ARG cc_start: 0.8504 (mtm180) cc_final: 0.8285 (mtm-85) REVERT: C 848 ASP cc_start: 0.7519 (m-30) cc_final: 0.7215 (m-30) REVERT: C 878 ASP cc_start: 0.7776 (p0) cc_final: 0.7510 (p0) REVERT: C 943 ILE cc_start: 0.8890 (mm) cc_final: 0.8678 (mt) REVERT: C 1000 ASN cc_start: 0.8486 (m110) cc_final: 0.8242 (m110) REVERT: C 1095 ASP cc_start: 0.7995 (t0) cc_final: 0.7567 (t0) REVERT: C 1096 ILE cc_start: 0.8646 (tp) cc_final: 0.8396 (tp) REVERT: C 1105 ARG cc_start: 0.8317 (tpp80) cc_final: 0.8053 (tpp80) REVERT: B 164 LYS cc_start: 0.8296 (mmmt) cc_final: 0.7954 (mmmt) REVERT: B 643 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7423 (p0) REVERT: B 644 TRP cc_start: 0.8517 (p90) cc_final: 0.7909 (p90) REVERT: B 732 SER cc_start: 0.8830 (p) cc_final: 0.8565 (m) REVERT: B 780 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 813 ASP cc_start: 0.7754 (t0) cc_final: 0.7536 (t0) REVERT: B 825 CYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6404 (t) REVERT: B 866 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8564 (p) REVERT: B 885 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8106 (pttm) REVERT: B 999 LYS cc_start: 0.8504 (mtpt) cc_final: 0.8295 (mtpp) REVERT: B 1010 LYS cc_start: 0.8539 (ttmm) cc_final: 0.8275 (ttmm) REVERT: B 1164 LEU cc_start: 0.8541 (mm) cc_final: 0.8242 (mp) REVERT: B 1174 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7882 (mm-40) REVERT: G 355 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5890 (mt) outliers start: 78 outliers final: 42 residues processed: 628 average time/residue: 0.3878 time to fit residues: 397.2053 Evaluate side-chains 591 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 543 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 886 SER Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 1041 ASN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 825 CYS Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 885 LYS Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 187 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 191 optimal weight: 1.9990 chunk 364 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 243 ASN A 799 HIS A 863 GLN C 445 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 998 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1180 GLN G 377 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.186859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135260 restraints weight = 52961.531| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.44 r_work: 0.3405 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31475 Z= 0.177 Angle : 0.544 18.299 43047 Z= 0.280 Chirality : 0.044 0.306 4968 Planarity : 0.004 0.051 5477 Dihedral : 4.626 56.084 4995 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.18 % Allowed : 11.01 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3922 helix: 1.54 (0.20), residues: 768 sheet: -0.26 (0.17), residues: 800 loop : -2.11 (0.12), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 444 HIS 0.011 0.001 HIS C1145 PHE 0.026 0.002 PHE A 67 TYR 0.022 0.002 TYR B 622 ARG 0.007 0.000 ARG C 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 24) link_NAG-ASN : angle 3.12876 ( 72) link_BETA1-4 : bond 0.00358 ( 12) link_BETA1-4 : angle 1.24183 ( 36) hydrogen bonds : bond 0.04935 ( 998) hydrogen bonds : angle 4.54452 ( 2772) SS BOND : bond 0.00228 ( 64) SS BOND : angle 1.33590 ( 128) covalent geometry : bond 0.00415 (31375) covalent geometry : angle 0.52381 (42811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 556 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8108 (t0) cc_final: 0.7871 (t0) REVERT: A 186 LYS cc_start: 0.8791 (ptmt) cc_final: 0.8547 (ttpt) REVERT: A 264 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7729 (mtm-85) REVERT: A 318 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.6019 (t80) REVERT: A 659 LYS cc_start: 0.6890 (tttt) cc_final: 0.6592 (tttt) REVERT: A 736 LEU cc_start: 0.8705 (mt) cc_final: 0.8457 (mp) REVERT: A 1049 ASN cc_start: 0.8586 (m-40) cc_final: 0.8349 (m-40) REVERT: A 1105 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7930 (ttt-90) REVERT: C 64 THR cc_start: 0.8581 (p) cc_final: 0.8296 (p) REVERT: C 75 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.5934 (pmt-80) REVERT: C 258 VAL cc_start: 0.8083 (m) cc_final: 0.7585 (p) REVERT: C 263 ARG cc_start: 0.8288 (ttt90) cc_final: 0.7981 (ttm110) REVERT: C 280 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (p) REVERT: C 296 SER cc_start: 0.8880 (m) cc_final: 0.8666 (t) REVERT: C 623 ASP cc_start: 0.8205 (t0) cc_final: 0.7999 (t70) REVERT: C 649 TYR cc_start: 0.8021 (m-80) cc_final: 0.7740 (m-80) REVERT: C 662 LEU cc_start: 0.8631 (mt) cc_final: 0.8366 (mp) REVERT: C 666 THR cc_start: 0.8319 (p) cc_final: 0.8077 (p) REVERT: C 700 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8563 (p) REVERT: C 763 ARG cc_start: 0.8624 (mtm180) cc_final: 0.8385 (mtm-85) REVERT: C 848 ASP cc_start: 0.7609 (m-30) cc_final: 0.7345 (m-30) REVERT: C 878 ASP cc_start: 0.7913 (p0) cc_final: 0.7646 (p0) REVERT: C 883 ASP cc_start: 0.8346 (t0) cc_final: 0.8044 (t70) REVERT: C 913 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 1000 ASN cc_start: 0.8514 (m110) cc_final: 0.8267 (m110) REVERT: C 1095 ASP cc_start: 0.7992 (t0) cc_final: 0.7611 (t0) REVERT: C 1096 ILE cc_start: 0.8632 (tp) cc_final: 0.8361 (tp) REVERT: C 1170 ILE cc_start: 0.8574 (mm) cc_final: 0.7877 (tt) REVERT: B 145 ILE cc_start: 0.8736 (mm) cc_final: 0.8326 (mt) REVERT: B 164 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8032 (mmmt) REVERT: B 238 MET cc_start: 0.7188 (mmm) cc_final: 0.6965 (mmm) REVERT: B 261 LEU cc_start: 0.8758 (mt) cc_final: 0.8504 (mp) REVERT: B 320 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8083 (ttm-80) REVERT: B 712 TYR cc_start: 0.8607 (p90) cc_final: 0.8382 (p90) REVERT: B 735 ASP cc_start: 0.7754 (t0) cc_final: 0.7456 (t0) REVERT: B 780 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 813 ASP cc_start: 0.7909 (t0) cc_final: 0.7603 (t0) REVERT: B 844 ASN cc_start: 0.8180 (m-40) cc_final: 0.7965 (m-40) REVERT: B 866 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 999 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8322 (mtpp) REVERT: B 1010 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8315 (ttmm) REVERT: B 1058 LEU cc_start: 0.8756 (mp) cc_final: 0.8515 (mt) REVERT: B 1164 LEU cc_start: 0.8620 (mm) cc_final: 0.8345 (mp) REVERT: B 1174 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8017 (mm-40) REVERT: T 349 MET cc_start: 0.0208 (mtt) cc_final: -0.0029 (mtt) REVERT: G 355 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5892 (mt) outliers start: 105 outliers final: 60 residues processed: 620 average time/residue: 0.4034 time to fit residues: 404.0292 Evaluate side-chains 598 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 531 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 960 THR Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 819 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1121 ILE Chi-restraints excluded: chain B residue 1198 SER Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 340 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 284 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 302 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 367 optimal weight: 40.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS B 941 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132129 restraints weight = 52950.222| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.41 r_work: 0.3351 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31475 Z= 0.228 Angle : 0.583 18.553 43047 Z= 0.303 Chirality : 0.046 0.205 4968 Planarity : 0.004 0.054 5477 Dihedral : 4.670 56.715 4993 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.42 % Allowed : 11.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3922 helix: 1.56 (0.20), residues: 763 sheet: -0.35 (0.17), residues: 821 loop : -2.06 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 444 HIS 0.025 0.002 HIS B 201 PHE 0.033 0.002 PHE A 222 TYR 0.024 0.002 TYR B 622 ARG 0.006 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 24) link_NAG-ASN : angle 3.20000 ( 72) link_BETA1-4 : bond 0.00343 ( 12) link_BETA1-4 : angle 1.07094 ( 36) hydrogen bonds : bond 0.05691 ( 998) hydrogen bonds : angle 4.71422 ( 2772) SS BOND : bond 0.00348 ( 64) SS BOND : angle 1.53616 ( 128) covalent geometry : bond 0.00530 (31375) covalent geometry : angle 0.56256 (42811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 574 time to evaluate : 3.086 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 42 VAL cc_start: 0.7553 (m) cc_final: 0.6939 (p) REVERT: A 318 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6039 (t80) REVERT: A 659 LYS cc_start: 0.7131 (tttt) cc_final: 0.6768 (tttt) REVERT: A 831 GLU cc_start: 0.7601 (mp0) cc_final: 0.7397 (mt-10) REVERT: A 880 ASP cc_start: 0.8190 (m-30) cc_final: 0.7962 (m-30) REVERT: A 915 ASP cc_start: 0.7737 (t0) cc_final: 0.7445 (t0) REVERT: A 1038 GLN cc_start: 0.8517 (tt0) cc_final: 0.8212 (tt0) REVERT: A 1076 ARG cc_start: 0.7676 (mtm-85) cc_final: 0.7422 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.7960 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7187 (t0) cc_final: 0.6532 (t0) REVERT: C 258 VAL cc_start: 0.8226 (m) cc_final: 0.7917 (p) REVERT: C 263 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8090 (ttm110) REVERT: C 280 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (p) REVERT: C 296 SER cc_start: 0.8887 (m) cc_final: 0.8668 (t) REVERT: C 623 ASP cc_start: 0.8194 (t0) cc_final: 0.7812 (t70) REVERT: C 700 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 763 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8435 (mtm-85) REVERT: C 848 ASP cc_start: 0.7637 (m-30) cc_final: 0.7402 (m-30) REVERT: C 878 ASP cc_start: 0.7980 (p0) cc_final: 0.7730 (p0) REVERT: C 883 ASP cc_start: 0.8380 (t0) cc_final: 0.8073 (t70) REVERT: C 913 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8545 (mt) REVERT: C 931 ILE cc_start: 0.4632 (OUTLIER) cc_final: 0.4351 (mm) REVERT: C 1000 ASN cc_start: 0.8505 (m110) cc_final: 0.8258 (m110) REVERT: C 1015 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 1095 ASP cc_start: 0.7951 (t0) cc_final: 0.7553 (t0) REVERT: C 1214 LYS cc_start: 0.8027 (tptt) cc_final: 0.7726 (tptt) REVERT: B 145 ILE cc_start: 0.8851 (mm) cc_final: 0.8492 (mt) REVERT: B 158 TYR cc_start: 0.7740 (m-10) cc_final: 0.7508 (m-80) REVERT: B 164 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8059 (mmmt) REVERT: B 188 ASN cc_start: 0.7610 (m-40) cc_final: 0.7345 (m110) REVERT: B 197 TRP cc_start: 0.8762 (m-90) cc_final: 0.8526 (m-90) REVERT: B 238 MET cc_start: 0.7268 (mmm) cc_final: 0.7052 (mmm) REVERT: B 272 GLU cc_start: 0.7574 (pm20) cc_final: 0.7331 (pm20) REVERT: B 320 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8182 (ttm-80) REVERT: B 712 TYR cc_start: 0.8735 (p90) cc_final: 0.8274 (p90) REVERT: B 735 ASP cc_start: 0.7789 (t0) cc_final: 0.7400 (t0) REVERT: B 813 ASP cc_start: 0.8014 (t0) cc_final: 0.7762 (t0) REVERT: B 866 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8561 (p) REVERT: B 920 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 999 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8336 (mtpp) REVERT: B 1010 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8272 (ttmm) REVERT: B 1058 LEU cc_start: 0.8800 (mp) cc_final: 0.8547 (mt) REVERT: B 1065 LEU cc_start: 0.8763 (mt) cc_final: 0.8489 (mt) REVERT: B 1164 LEU cc_start: 0.8729 (mm) cc_final: 0.8439 (mp) REVERT: B 1174 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8095 (mm-40) REVERT: G 355 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5909 (mt) outliers start: 113 outliers final: 79 residues processed: 643 average time/residue: 0.4071 time to fit residues: 421.8171 Evaluate side-chains 648 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 561 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1198 SER Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 326 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 276 optimal weight: 0.6980 chunk 347 optimal weight: 50.0000 chunk 383 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 364 optimal weight: 0.8980 chunk 380 optimal weight: 50.0000 chunk 366 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 870 ASN ** B1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.185855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134626 restraints weight = 52342.522| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.91 r_work: 0.3425 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 31475 Z= 0.133 Angle : 0.547 18.193 43047 Z= 0.279 Chirality : 0.044 0.185 4968 Planarity : 0.004 0.047 5477 Dihedral : 4.429 55.200 4992 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.96 % Allowed : 13.00 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.13), residues: 3922 helix: 1.71 (0.20), residues: 760 sheet: -0.26 (0.17), residues: 827 loop : -1.95 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 444 HIS 0.010 0.001 HIS B 201 PHE 0.028 0.001 PHE B 185 TYR 0.026 0.001 TYR A 625 ARG 0.005 0.000 ARG C1076 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 24) link_NAG-ASN : angle 3.09683 ( 72) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 0.99877 ( 36) hydrogen bonds : bond 0.04697 ( 998) hydrogen bonds : angle 4.56781 ( 2772) SS BOND : bond 0.00250 ( 64) SS BOND : angle 1.75362 ( 128) covalent geometry : bond 0.00312 (31375) covalent geometry : angle 0.52394 (42811) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 553 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8228 (p90) cc_final: 0.8025 (p90) REVERT: A 221 THR cc_start: 0.8559 (p) cc_final: 0.8276 (p) REVERT: A 264 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7775 (mtm-85) REVERT: A 318 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5980 (t80) REVERT: A 659 LYS cc_start: 0.7030 (tttt) cc_final: 0.6688 (tttt) REVERT: A 880 ASP cc_start: 0.8140 (m-30) cc_final: 0.7939 (m-30) REVERT: A 1038 GLN cc_start: 0.8415 (tt0) cc_final: 0.8132 (tt0) REVERT: A 1076 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7214 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7876 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7148 (t0) cc_final: 0.6470 (t0) REVERT: C 75 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5855 (pmt-80) REVERT: C 212 TYR cc_start: 0.7376 (m-80) cc_final: 0.7050 (m-80) REVERT: C 258 VAL cc_start: 0.8098 (m) cc_final: 0.7660 (p) REVERT: C 263 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8123 (ttm110) REVERT: C 296 SER cc_start: 0.8841 (m) cc_final: 0.8626 (t) REVERT: C 623 ASP cc_start: 0.8014 (t0) cc_final: 0.7769 (t70) REVERT: C 700 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8598 (p) REVERT: C 763 ARG cc_start: 0.8656 (mtm180) cc_final: 0.8401 (mtm-85) REVERT: C 848 ASP cc_start: 0.7563 (m-30) cc_final: 0.7316 (m-30) REVERT: C 878 ASP cc_start: 0.7966 (p0) cc_final: 0.7704 (p0) REVERT: C 883 ASP cc_start: 0.8299 (t0) cc_final: 0.7981 (t70) REVERT: C 913 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8493 (mt) REVERT: C 931 ILE cc_start: 0.4608 (OUTLIER) cc_final: 0.4286 (mm) REVERT: C 1000 ASN cc_start: 0.8422 (m110) cc_final: 0.8151 (m110) REVERT: C 1015 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 1063 SER cc_start: 0.8254 (m) cc_final: 0.7851 (p) REVERT: C 1095 ASP cc_start: 0.7891 (t0) cc_final: 0.7502 (t0) REVERT: C 1170 ILE cc_start: 0.8562 (mm) cc_final: 0.7843 (tt) REVERT: B 73 ASN cc_start: 0.7504 (m-40) cc_final: 0.7201 (m-40) REVERT: B 145 ILE cc_start: 0.8831 (mm) cc_final: 0.8475 (mt) REVERT: B 158 TYR cc_start: 0.7642 (m-10) cc_final: 0.7409 (m-80) REVERT: B 164 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8045 (mmmt) REVERT: B 174 TRP cc_start: 0.7695 (p-90) cc_final: 0.7306 (p-90) REVERT: B 197 TRP cc_start: 0.8707 (m-90) cc_final: 0.8492 (m-90) REVERT: B 238 MET cc_start: 0.7174 (mmm) cc_final: 0.6950 (mmm) REVERT: B 712 TYR cc_start: 0.8713 (p90) cc_final: 0.8189 (p90) REVERT: B 735 ASP cc_start: 0.7776 (t0) cc_final: 0.7362 (t0) REVERT: B 866 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 999 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8280 (mtpp) REVERT: B 1010 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8200 (ttmm) REVERT: B 1058 LEU cc_start: 0.8709 (mp) cc_final: 0.8468 (mt) REVERT: B 1065 LEU cc_start: 0.8782 (mt) cc_final: 0.8574 (mt) REVERT: B 1164 LEU cc_start: 0.8706 (mm) cc_final: 0.8418 (mp) REVERT: B 1174 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8039 (mm-40) REVERT: G 355 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5743 (mt) outliers start: 98 outliers final: 62 residues processed: 607 average time/residue: 0.4088 time to fit residues: 400.1308 Evaluate side-chains 609 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 539 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1198 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1015 ILE Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1198 SER Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 132 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 359 optimal weight: 50.0000 chunk 116 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 193 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 652 ASN ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN C 323 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 998 ASN B1180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.185179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133054 restraints weight = 52798.929| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.08 r_work: 0.3402 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 31475 Z= 0.143 Angle : 0.545 17.877 43047 Z= 0.279 Chirality : 0.044 0.238 4968 Planarity : 0.004 0.048 5477 Dihedral : 4.358 55.226 4991 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.99 % Allowed : 13.55 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3922 helix: 1.77 (0.20), residues: 760 sheet: -0.26 (0.18), residues: 796 loop : -1.87 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 257 HIS 0.010 0.001 HIS B 160 PHE 0.022 0.001 PHE A 711 TYR 0.023 0.001 TYR B 622 ARG 0.004 0.000 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 24) link_NAG-ASN : angle 3.15434 ( 72) link_BETA1-4 : bond 0.00363 ( 12) link_BETA1-4 : angle 0.98673 ( 36) hydrogen bonds : bond 0.04705 ( 998) hydrogen bonds : angle 4.54908 ( 2772) SS BOND : bond 0.00237 ( 64) SS BOND : angle 1.65074 ( 128) covalent geometry : bond 0.00337 (31375) covalent geometry : angle 0.52269 (42811) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 553 time to evaluate : 3.386 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 221 THR cc_start: 0.8553 (p) cc_final: 0.8281 (p) REVERT: A 318 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 630 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7562 (mm-40) REVERT: A 659 LYS cc_start: 0.7017 (tttt) cc_final: 0.6671 (tttt) REVERT: A 834 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7150 (m) REVERT: A 1038 GLN cc_start: 0.8436 (tt0) cc_final: 0.8135 (tt0) REVERT: A 1076 ARG cc_start: 0.7510 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7917 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7207 (t0) cc_final: 0.6547 (t0) REVERT: C 75 ARG cc_start: 0.6430 (OUTLIER) cc_final: 0.5948 (pmt-80) REVERT: C 258 VAL cc_start: 0.8077 (m) cc_final: 0.7625 (p) REVERT: C 283 SER cc_start: 0.9029 (t) cc_final: 0.8625 (t) REVERT: C 296 SER cc_start: 0.8844 (m) cc_final: 0.8632 (t) REVERT: C 623 ASP cc_start: 0.7987 (t0) cc_final: 0.7732 (t70) REVERT: C 700 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8587 (p) REVERT: C 763 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8314 (mtm110) REVERT: C 828 LEU cc_start: 0.9085 (tp) cc_final: 0.8834 (tt) REVERT: C 848 ASP cc_start: 0.7562 (m-30) cc_final: 0.7306 (m-30) REVERT: C 878 ASP cc_start: 0.7973 (p0) cc_final: 0.7708 (p0) REVERT: C 883 ASP cc_start: 0.8327 (t0) cc_final: 0.8018 (t70) REVERT: C 913 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8502 (mt) REVERT: C 931 ILE cc_start: 0.4603 (OUTLIER) cc_final: 0.4288 (mm) REVERT: C 1000 ASN cc_start: 0.8441 (m110) cc_final: 0.8177 (m110) REVERT: C 1015 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8374 (mt) REVERT: C 1063 SER cc_start: 0.8266 (m) cc_final: 0.7818 (p) REVERT: C 1095 ASP cc_start: 0.7902 (t0) cc_final: 0.7509 (t0) REVERT: C 1168 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7438 (mtm-85) REVERT: C 1170 ILE cc_start: 0.8541 (mm) cc_final: 0.7832 (tt) REVERT: B 73 ASN cc_start: 0.7532 (m-40) cc_final: 0.7217 (m-40) REVERT: B 145 ILE cc_start: 0.8836 (mm) cc_final: 0.8495 (mt) REVERT: B 158 TYR cc_start: 0.7654 (m-10) cc_final: 0.7394 (m-80) REVERT: B 164 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8057 (mmmt) REVERT: B 174 TRP cc_start: 0.7722 (p-90) cc_final: 0.7295 (p-90) REVERT: B 197 TRP cc_start: 0.8717 (m-90) cc_final: 0.8498 (m-90) REVERT: B 238 MET cc_start: 0.7224 (mmm) cc_final: 0.6977 (mmm) REVERT: B 712 TYR cc_start: 0.8751 (p90) cc_final: 0.8209 (p90) REVERT: B 735 ASP cc_start: 0.7799 (t0) cc_final: 0.7343 (t0) REVERT: B 866 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 999 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8311 (mtpp) REVERT: B 1010 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8186 (ttmm) REVERT: B 1058 LEU cc_start: 0.8704 (mp) cc_final: 0.8477 (mt) REVERT: B 1065 LEU cc_start: 0.8776 (mt) cc_final: 0.8563 (mt) REVERT: B 1164 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 1174 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8049 (mm-40) REVERT: G 355 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5930 (mt) outliers start: 99 outliers final: 73 residues processed: 609 average time/residue: 0.4085 time to fit residues: 402.6214 Evaluate side-chains 621 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 538 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 998 ASN Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1198 SER Chi-restraints excluded: chain B residue 1214 LYS Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 324 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 chunk 47 optimal weight: 30.0000 chunk 192 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 35 optimal weight: 0.0000 chunk 41 optimal weight: 30.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A 876 HIS A1049 ASN C 188 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 876 HIS B 998 ASN B1180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.185036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133678 restraints weight = 52521.673| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.83 r_work: 0.3423 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31475 Z= 0.142 Angle : 0.548 17.581 43047 Z= 0.280 Chirality : 0.044 0.464 4968 Planarity : 0.004 0.049 5477 Dihedral : 4.401 54.780 4991 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.05 % Allowed : 13.73 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 3922 helix: 1.76 (0.20), residues: 763 sheet: -0.23 (0.18), residues: 794 loop : -1.84 (0.12), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 257 HIS 0.011 0.001 HIS B 160 PHE 0.023 0.001 PHE A 711 TYR 0.027 0.001 TYR A 191 ARG 0.007 0.000 ARG A 264 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 24) link_NAG-ASN : angle 3.33493 ( 72) link_BETA1-4 : bond 0.00374 ( 12) link_BETA1-4 : angle 0.97617 ( 36) hydrogen bonds : bond 0.04677 ( 998) hydrogen bonds : angle 4.55027 ( 2772) SS BOND : bond 0.00268 ( 64) SS BOND : angle 1.72541 ( 128) covalent geometry : bond 0.00334 (31375) covalent geometry : angle 0.52323 (42811) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 541 time to evaluate : 3.177 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 221 THR cc_start: 0.8668 (p) cc_final: 0.8406 (p) REVERT: A 318 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6179 (t80) REVERT: A 630 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7590 (mm110) REVERT: A 659 LYS cc_start: 0.7167 (tttt) cc_final: 0.6829 (tttt) REVERT: A 834 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7312 (m) REVERT: A 1038 GLN cc_start: 0.8618 (tt0) cc_final: 0.8322 (tt0) REVERT: A 1076 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7545 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.8160 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7522 (t0) cc_final: 0.6931 (t0) REVERT: C 75 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5987 (pmt-80) REVERT: C 258 VAL cc_start: 0.8091 (m) cc_final: 0.7641 (p) REVERT: C 271 ASP cc_start: 0.7045 (p0) cc_final: 0.6648 (p0) REVERT: C 283 SER cc_start: 0.9013 (t) cc_final: 0.8633 (t) REVERT: C 296 SER cc_start: 0.8924 (m) cc_final: 0.8709 (t) REVERT: C 321 ILE cc_start: 0.8085 (mm) cc_final: 0.7844 (mm) REVERT: C 623 ASP cc_start: 0.8254 (t0) cc_final: 0.7975 (t70) REVERT: C 828 LEU cc_start: 0.9130 (tp) cc_final: 0.8865 (tt) REVERT: C 848 ASP cc_start: 0.7870 (m-30) cc_final: 0.7632 (m-30) REVERT: C 878 ASP cc_start: 0.8103 (p0) cc_final: 0.7876 (p0) REVERT: C 913 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (mt) REVERT: C 931 ILE cc_start: 0.4763 (OUTLIER) cc_final: 0.4428 (mm) REVERT: C 1000 ASN cc_start: 0.8608 (m110) cc_final: 0.8358 (m110) REVERT: C 1015 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8446 (mt) REVERT: C 1063 SER cc_start: 0.8353 (m) cc_final: 0.7967 (p) REVERT: C 1095 ASP cc_start: 0.8223 (t0) cc_final: 0.7843 (t0) REVERT: C 1168 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: B 73 ASN cc_start: 0.7667 (m-40) cc_final: 0.7348 (m-40) REVERT: B 145 ILE cc_start: 0.8915 (mm) cc_final: 0.8591 (mt) REVERT: B 158 TYR cc_start: 0.7755 (m-10) cc_final: 0.7489 (m-80) REVERT: B 164 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8148 (mmmt) REVERT: B 174 TRP cc_start: 0.7849 (p-90) cc_final: 0.7434 (p-90) REVERT: B 197 TRP cc_start: 0.8774 (m-90) cc_final: 0.8549 (m-90) REVERT: B 238 MET cc_start: 0.7547 (mmm) cc_final: 0.7312 (mmm) REVERT: B 712 TYR cc_start: 0.8872 (p90) cc_final: 0.8301 (p90) REVERT: B 735 ASP cc_start: 0.8063 (t0) cc_final: 0.7610 (t0) REVERT: B 845 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: B 866 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 996 VAL cc_start: 0.8742 (m) cc_final: 0.8451 (p) REVERT: B 999 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8393 (mtpp) REVERT: B 1010 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8389 (ttmm) REVERT: B 1058 LEU cc_start: 0.8830 (mp) cc_final: 0.8598 (mt) REVERT: B 1065 LEU cc_start: 0.8825 (mt) cc_final: 0.8518 (mt) REVERT: B 1112 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 1164 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8450 (mp) REVERT: B 1167 ASP cc_start: 0.7820 (t0) cc_final: 0.7275 (t0) REVERT: B 1174 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8261 (mm-40) REVERT: G 355 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5805 (mt) outliers start: 101 outliers final: 76 residues processed: 599 average time/residue: 0.4020 time to fit residues: 387.7790 Evaluate side-chains 622 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 536 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 872 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1198 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1198 SER Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 212 optimal weight: 0.9990 chunk 290 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 274 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 386 optimal weight: 0.2980 chunk 109 optimal weight: 20.0000 chunk 331 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 334 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 863 GLN A1045 GLN C 323 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS B1180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.185798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133942 restraints weight = 52647.043| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.98 r_work: 0.3402 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31475 Z= 0.114 Angle : 0.661 58.335 43047 Z= 0.351 Chirality : 0.043 0.256 4968 Planarity : 0.004 0.073 5477 Dihedral : 4.590 54.481 4991 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.07 % Favored : 94.90 % Rotamer: Outliers : 2.96 % Allowed : 14.06 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3922 helix: 1.82 (0.20), residues: 763 sheet: -0.23 (0.17), residues: 818 loop : -1.79 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 257 HIS 0.012 0.001 HIS B 160 PHE 0.024 0.001 PHE A 711 TYR 0.025 0.001 TYR B 622 ARG 0.012 0.000 ARG A 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 24) link_NAG-ASN : angle 3.96785 ( 72) link_BETA1-4 : bond 0.00359 ( 12) link_BETA1-4 : angle 0.97553 ( 36) hydrogen bonds : bond 0.04416 ( 998) hydrogen bonds : angle 4.51597 ( 2772) SS BOND : bond 0.00240 ( 64) SS BOND : angle 1.58124 ( 128) covalent geometry : bond 0.00267 (31375) covalent geometry : angle 0.63596 (42811) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 539 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8179 (t0) cc_final: 0.7935 (t0) REVERT: A 186 LYS cc_start: 0.8820 (ptmt) cc_final: 0.8554 (ttpt) REVERT: A 221 THR cc_start: 0.8543 (p) cc_final: 0.8269 (p) REVERT: A 318 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6024 (t80) REVERT: A 630 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7486 (mm110) REVERT: A 659 LYS cc_start: 0.7001 (tttt) cc_final: 0.6696 (tttt) REVERT: A 834 THR cc_start: 0.7325 (OUTLIER) cc_final: 0.7079 (m) REVERT: A 1038 GLN cc_start: 0.8406 (tt0) cc_final: 0.8125 (tt0) REVERT: A 1076 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.7205 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8186 (ttm-80) cc_final: 0.7927 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7278 (t0) cc_final: 0.6646 (t0) REVERT: C 64 THR cc_start: 0.8583 (p) cc_final: 0.8316 (p) REVERT: C 75 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5914 (pmt-80) REVERT: C 271 ASP cc_start: 0.6862 (p0) cc_final: 0.6494 (p0) REVERT: C 283 SER cc_start: 0.8901 (t) cc_final: 0.8508 (t) REVERT: C 296 SER cc_start: 0.8831 (m) cc_final: 0.8615 (t) REVERT: C 321 ILE cc_start: 0.7953 (mm) cc_final: 0.7730 (mm) REVERT: C 623 ASP cc_start: 0.7958 (t0) cc_final: 0.7685 (t70) REVERT: C 828 LEU cc_start: 0.9093 (tp) cc_final: 0.8808 (tt) REVERT: C 848 ASP cc_start: 0.7543 (m-30) cc_final: 0.7283 (m-30) REVERT: C 878 ASP cc_start: 0.7952 (p0) cc_final: 0.7712 (p0) REVERT: C 913 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8504 (mt) REVERT: C 931 ILE cc_start: 0.4619 (OUTLIER) cc_final: 0.4295 (mm) REVERT: C 1000 ASN cc_start: 0.8405 (m110) cc_final: 0.8147 (m110) REVERT: C 1015 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8364 (mt) REVERT: C 1063 SER cc_start: 0.8245 (m) cc_final: 0.7811 (p) REVERT: C 1095 ASP cc_start: 0.7895 (t0) cc_final: 0.7508 (t0) REVERT: C 1168 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7432 (mtm-85) REVERT: B 73 ASN cc_start: 0.7510 (m-40) cc_final: 0.7187 (m-40) REVERT: B 145 ILE cc_start: 0.8850 (mm) cc_final: 0.8517 (mt) REVERT: B 158 TYR cc_start: 0.7633 (m-10) cc_final: 0.7362 (m-80) REVERT: B 164 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8037 (mmmt) REVERT: B 174 TRP cc_start: 0.7682 (p-90) cc_final: 0.7238 (p-90) REVERT: B 197 TRP cc_start: 0.8689 (m-90) cc_final: 0.8480 (m-90) REVERT: B 238 MET cc_start: 0.7194 (mmm) cc_final: 0.6975 (mmm) REVERT: B 712 TYR cc_start: 0.8765 (p90) cc_final: 0.8242 (p90) REVERT: B 735 ASP cc_start: 0.7812 (t0) cc_final: 0.7345 (t0) REVERT: B 866 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8528 (p) REVERT: B 905 ASP cc_start: 0.7829 (m-30) cc_final: 0.7564 (m-30) REVERT: B 996 VAL cc_start: 0.8652 (m) cc_final: 0.8355 (p) REVERT: B 999 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8253 (mtpp) REVERT: B 1010 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8190 (ttmm) REVERT: B 1058 LEU cc_start: 0.8669 (mp) cc_final: 0.8445 (mt) REVERT: B 1065 LEU cc_start: 0.8761 (mt) cc_final: 0.8454 (mt) REVERT: B 1164 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 1167 ASP cc_start: 0.7608 (t0) cc_final: 0.7064 (t0) REVERT: B 1174 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8058 (mm-40) REVERT: G 355 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5771 (mt) outliers start: 98 outliers final: 73 residues processed: 593 average time/residue: 0.4089 time to fit residues: 391.0742 Evaluate side-chains 611 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 529 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 872 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1198 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 831 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 315 optimal weight: 0.0370 chunk 306 optimal weight: 0.7980 chunk 336 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 383 optimal weight: 20.0000 chunk 226 optimal weight: 0.9980 chunk 295 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 358 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133488 restraints weight = 52671.166| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.10 r_work: 0.3406 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31475 Z= 0.126 Angle : 0.664 56.971 43047 Z= 0.354 Chirality : 0.043 0.270 4968 Planarity : 0.004 0.062 5477 Dihedral : 4.516 54.475 4991 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.66 % Allowed : 14.42 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3922 helix: 1.81 (0.20), residues: 763 sheet: -0.21 (0.17), residues: 809 loop : -1.78 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 257 HIS 0.011 0.001 HIS B 160 PHE 0.023 0.001 PHE A 711 TYR 0.028 0.001 TYR B 649 ARG 0.014 0.000 ARG A 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 24) link_NAG-ASN : angle 4.12841 ( 72) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 0.96867 ( 36) hydrogen bonds : bond 0.04436 ( 998) hydrogen bonds : angle 4.51560 ( 2772) SS BOND : bond 0.00270 ( 64) SS BOND : angle 1.71708 ( 128) covalent geometry : bond 0.00296 (31375) covalent geometry : angle 0.63694 (42811) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 529 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8205 (t0) cc_final: 0.7958 (t0) REVERT: A 152 GLN cc_start: 0.7244 (tp-100) cc_final: 0.6963 (tp40) REVERT: A 186 LYS cc_start: 0.8847 (ptmt) cc_final: 0.8584 (ttpt) REVERT: A 221 THR cc_start: 0.8569 (p) cc_final: 0.8292 (p) REVERT: A 318 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.6037 (t80) REVERT: A 630 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7503 (mm110) REVERT: A 659 LYS cc_start: 0.7014 (tttt) cc_final: 0.6704 (tttt) REVERT: A 834 THR cc_start: 0.7362 (OUTLIER) cc_final: 0.7126 (m) REVERT: A 1038 GLN cc_start: 0.8461 (tt0) cc_final: 0.8179 (tt0) REVERT: A 1105 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.8019 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7290 (t0) cc_final: 0.6683 (t0) REVERT: C 64 THR cc_start: 0.8586 (p) cc_final: 0.8322 (p) REVERT: C 75 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5899 (pmt-80) REVERT: C 271 ASP cc_start: 0.6877 (p0) cc_final: 0.6511 (p0) REVERT: C 283 SER cc_start: 0.8877 (t) cc_final: 0.8488 (t) REVERT: C 296 SER cc_start: 0.8835 (m) cc_final: 0.8623 (t) REVERT: C 623 ASP cc_start: 0.7972 (t0) cc_final: 0.7708 (t70) REVERT: C 828 LEU cc_start: 0.9100 (tp) cc_final: 0.8789 (tt) REVERT: C 848 ASP cc_start: 0.7566 (m-30) cc_final: 0.7307 (m-30) REVERT: C 878 ASP cc_start: 0.7974 (p0) cc_final: 0.7725 (p0) REVERT: C 913 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8508 (mt) REVERT: C 931 ILE cc_start: 0.4626 (OUTLIER) cc_final: 0.4299 (mm) REVERT: C 1000 ASN cc_start: 0.8404 (m110) cc_final: 0.8150 (m110) REVERT: C 1015 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8392 (mt) REVERT: C 1063 SER cc_start: 0.8238 (m) cc_final: 0.7839 (p) REVERT: C 1095 ASP cc_start: 0.7914 (t0) cc_final: 0.7539 (t0) REVERT: C 1168 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: B 73 ASN cc_start: 0.7536 (m-40) cc_final: 0.7215 (m-40) REVERT: B 145 ILE cc_start: 0.8864 (mm) cc_final: 0.8521 (mt) REVERT: B 158 TYR cc_start: 0.7609 (m-10) cc_final: 0.7346 (m-80) REVERT: B 164 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8062 (mmmt) REVERT: B 174 TRP cc_start: 0.7663 (p-90) cc_final: 0.7243 (p-90) REVERT: B 197 TRP cc_start: 0.8684 (m-90) cc_final: 0.8483 (m-90) REVERT: B 238 MET cc_start: 0.7220 (mmm) cc_final: 0.6996 (mmm) REVERT: B 712 TYR cc_start: 0.8777 (p90) cc_final: 0.8200 (p90) REVERT: B 735 ASP cc_start: 0.7827 (t0) cc_final: 0.7370 (t0) REVERT: B 866 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 905 ASP cc_start: 0.7826 (m-30) cc_final: 0.7565 (m-30) REVERT: B 996 VAL cc_start: 0.8662 (m) cc_final: 0.8374 (p) REVERT: B 999 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8270 (mtpp) REVERT: B 1002 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7794 (mmmm) REVERT: B 1010 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8224 (ttmm) REVERT: B 1058 LEU cc_start: 0.8695 (mp) cc_final: 0.8472 (mt) REVERT: B 1164 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 1167 ASP cc_start: 0.7637 (t0) cc_final: 0.7100 (t0) REVERT: B 1174 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8064 (mm-40) REVERT: G 355 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5814 (mt) outliers start: 88 outliers final: 75 residues processed: 579 average time/residue: 0.4222 time to fit residues: 392.8320 Evaluate side-chains 612 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 528 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 872 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1198 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 364 optimal weight: 40.0000 chunk 79 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 379 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.185212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133127 restraints weight = 52850.764| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.06 r_work: 0.3400 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31475 Z= 0.181 Angle : 0.676 55.940 43047 Z= 0.361 Chirality : 0.044 0.273 4968 Planarity : 0.004 0.061 5477 Dihedral : 4.567 54.669 4991 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.66 % Allowed : 14.42 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3922 helix: 1.74 (0.20), residues: 765 sheet: -0.22 (0.18), residues: 801 loop : -1.80 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 257 HIS 0.012 0.001 HIS B 160 PHE 0.024 0.001 PHE A 711 TYR 0.039 0.002 TYR B 649 ARG 0.014 0.000 ARG A 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 24) link_NAG-ASN : angle 4.04098 ( 72) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 0.95915 ( 36) hydrogen bonds : bond 0.04689 ( 998) hydrogen bonds : angle 4.52747 ( 2772) SS BOND : bond 0.00438 ( 64) SS BOND : angle 1.96689 ( 128) covalent geometry : bond 0.00423 (31375) covalent geometry : angle 0.64813 (42811) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7844 Ramachandran restraints generated. 3922 Oldfield, 0 Emsley, 3922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 533 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASN cc_start: 0.8201 (t0) cc_final: 0.7943 (t0) REVERT: A 152 GLN cc_start: 0.7279 (tp-100) cc_final: 0.6989 (tp40) REVERT: A 186 LYS cc_start: 0.8835 (ptmt) cc_final: 0.8528 (ttpt) REVERT: A 221 THR cc_start: 0.8553 (p) cc_final: 0.8282 (p) REVERT: A 318 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6031 (t80) REVERT: A 659 LYS cc_start: 0.7033 (tttt) cc_final: 0.6716 (tttt) REVERT: A 834 THR cc_start: 0.7387 (OUTLIER) cc_final: 0.7160 (m) REVERT: A 1038 GLN cc_start: 0.8423 (tt0) cc_final: 0.8153 (tt0) REVERT: A 1076 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7269 (mtm-85) REVERT: A 1105 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7951 (ttt-90) REVERT: A 1167 ASP cc_start: 0.7276 (t0) cc_final: 0.6694 (t0) REVERT: C 64 THR cc_start: 0.8584 (p) cc_final: 0.8320 (p) REVERT: C 75 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5939 (pmt-80) REVERT: C 271 ASP cc_start: 0.6872 (p0) cc_final: 0.6501 (p0) REVERT: C 283 SER cc_start: 0.8873 (t) cc_final: 0.8477 (t) REVERT: C 296 SER cc_start: 0.8851 (m) cc_final: 0.8631 (t) REVERT: C 623 ASP cc_start: 0.7957 (t0) cc_final: 0.7696 (t70) REVERT: C 828 LEU cc_start: 0.9099 (tp) cc_final: 0.8790 (tt) REVERT: C 848 ASP cc_start: 0.7594 (m-30) cc_final: 0.7342 (m-30) REVERT: C 878 ASP cc_start: 0.7980 (p0) cc_final: 0.7727 (p0) REVERT: C 913 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 931 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4303 (mm) REVERT: C 1000 ASN cc_start: 0.8412 (m110) cc_final: 0.8166 (m110) REVERT: C 1015 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 1063 SER cc_start: 0.8253 (m) cc_final: 0.7823 (p) REVERT: C 1095 ASP cc_start: 0.7887 (t0) cc_final: 0.7512 (t0) REVERT: C 1168 ARG cc_start: 0.7790 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: B 73 ASN cc_start: 0.7499 (m-40) cc_final: 0.7184 (m-40) REVERT: B 145 ILE cc_start: 0.8875 (mm) cc_final: 0.8537 (mt) REVERT: B 158 TYR cc_start: 0.7581 (m-10) cc_final: 0.7321 (m-80) REVERT: B 164 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8067 (mmmt) REVERT: B 174 TRP cc_start: 0.7676 (p-90) cc_final: 0.7258 (p-90) REVERT: B 238 MET cc_start: 0.7165 (mmm) cc_final: 0.6945 (mmm) REVERT: B 712 TYR cc_start: 0.8765 (p90) cc_final: 0.8191 (p90) REVERT: B 735 ASP cc_start: 0.7849 (t0) cc_final: 0.7381 (t0) REVERT: B 866 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8528 (p) REVERT: B 905 ASP cc_start: 0.7827 (m-30) cc_final: 0.7549 (m-30) REVERT: B 996 VAL cc_start: 0.8673 (m) cc_final: 0.8396 (p) REVERT: B 999 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8259 (mtpp) REVERT: B 1002 LYS cc_start: 0.8058 (mmmm) cc_final: 0.7820 (mmmm) REVERT: B 1010 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8205 (ttmm) REVERT: B 1058 LEU cc_start: 0.8691 (mp) cc_final: 0.8465 (mt) REVERT: B 1112 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 1164 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8441 (mp) REVERT: B 1167 ASP cc_start: 0.7631 (t0) cc_final: 0.7103 (t0) REVERT: B 1174 GLN cc_start: 0.8256 (mm-40) cc_final: 0.8041 (mm-40) REVERT: G 355 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5889 (mt) outliers start: 88 outliers final: 75 residues processed: 582 average time/residue: 0.3967 time to fit residues: 370.5646 Evaluate side-chains 614 residues out of total 3515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 530 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 201 HIS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1168 ARG Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 658 PHE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 831 GLU Chi-restraints excluded: chain C residue 872 ASN Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1162 LEU Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1173 LYS Chi-restraints excluded: chain C residue 1198 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 719 CYS Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1029 ILE Chi-restraints excluded: chain B residue 1114 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1218 ILE Chi-restraints excluded: chain T residue 298 VAL Chi-restraints excluded: chain T residue 387 THR Chi-restraints excluded: chain G residue 355 LEU Chi-restraints excluded: chain G residue 410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 75 optimal weight: 0.9990 chunk 384 optimal weight: 30.0000 chunk 339 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132044 restraints weight = 52618.511| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.26 r_work: 0.3357 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 31475 Z= 0.244 Angle : 0.711 56.473 43047 Z= 0.380 Chirality : 0.046 0.335 4968 Planarity : 0.004 0.054 5477 Dihedral : 4.692 55.090 4991 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.72 % Allowed : 14.64 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3922 helix: 1.69 (0.20), residues: 766 sheet: -0.21 (0.18), residues: 778 loop : -1.85 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 257 HIS 0.014 0.002 HIS B 160 PHE 0.029 0.002 PHE C 209 TYR 0.051 0.002 TYR B 649 ARG 0.015 0.001 ARG A 763 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 24) link_NAG-ASN : angle 3.99715 ( 72) link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 0.95243 ( 36) hydrogen bonds : bond 0.05296 ( 998) hydrogen bonds : angle 4.62136 ( 2772) SS BOND : bond 0.00324 ( 64) SS BOND : angle 1.99212 ( 128) covalent geometry : bond 0.00565 (31375) covalent geometry : angle 0.68502 (42811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17478.43 seconds wall clock time: 302 minutes 18.84 seconds (18138.84 seconds total)