Starting phenix.real_space_refine on Wed Aug 27 00:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhl_60107/08_2025/8zhl_60107.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6148 atoms to isotropic. 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 158 5.16 5 C 24542 2.51 5 N 6393 2.21 5 O 7683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.14s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38776 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8344 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 56, 'TRANS': 1009} Chain breaks: 5 Chain: "H" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1557 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1585 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain breaks: 1 Chain: "M" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1670 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: "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: "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: 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 9.37, per 1000 atoms: 0.24 Number of scatterers: 38776 At special positions: 0 Unit cell: (186, 217.248, 205.344, 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 158 16.00 O 7683 8.00 N 6393 7.00 C 24542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=58, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 91 " distance=2.03 Simple disulfide: pdb=" SG CYS K 145 " - pdb=" SG CYS K 204 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 147 " - pdb=" SG CYS M 203 " 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 F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG F 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 1.2 microseconds 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9184 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 99 sheets defined 14.7% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.910A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.988A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 782 removed outlier: 3.819A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.670A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.084A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.695A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.115A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.549A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.113A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.874A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 753 removed outlier: 4.023A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 782 removed outlier: 3.899A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.621A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.672A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.095A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 946 through 966 removed outlier: 3.853A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.013A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.209A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.506A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 752 removed outlier: 3.918A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 782 removed outlier: 3.784A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.726A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.068A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.663A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 916 removed outlier: 3.540A pdb=" N LEU C 916 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.577A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 966 removed outlier: 3.853A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.202A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.965A pdb=" N GLN L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN L 133 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 removed outlier: 3.971A pdb=" N LYS L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 200 No H-bonds generated for 'chain 'G' and resid 198 through 200' Processing helix chain 'I' and resid 129 through 133 removed outlier: 3.670A pdb=" N ASN I 133 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.057A pdb=" N LYS I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 132 through 138 Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.540A pdb=" N LYS D 197 " --> pdb=" O PRO D 193 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 4.089A pdb=" N GLY E 33 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR E 34 " --> pdb=" O SER E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 30 through 34' Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.875A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'K' and resid 132 through 138 Processing helix chain 'K' and resid 192 through 199 removed outlier: 3.566A pdb=" N LYS K 197 " --> pdb=" O PRO K 193 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS K 199 " --> pdb=" O GLN K 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 92 removed outlier: 3.925A pdb=" N THR M 92 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 138 removed outlier: 3.767A pdb=" N THR M 138 " --> pdb=" O SER M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 196 No H-bonds generated for 'chain 'M' and resid 194 through 196' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.334A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.732A pdb=" N GLU C 583 " --> pdb=" O ASP C 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.802A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.942A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 12.716A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.758A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.632A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.696A pdb=" N ARG A 466 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY H 104 " --> pdb=" O ARG A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.380A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.500A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.216A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.605A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.700A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.622A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.049A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.206A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.780A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.516A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.516A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.516A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.533A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.887A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 578 removed outlier: 3.534A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.555A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 666 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.499A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 727 removed outlier: 6.499A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.390A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.592A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.609A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.411A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.098A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.671A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.793A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 466 through 467 removed outlier: 3.668A pdb=" N ARG C 466 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY G 104 " --> pdb=" O ARG C 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.489A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.688A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 727 removed outlier: 3.808A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.192A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.501A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.405A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.669A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 52 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 57 " --> pdb=" O ILE H 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.107A pdb=" N LEU H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.525A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 195 " --> pdb=" O ALA H 147 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER H 191 " --> pdb=" O CYS H 151 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL H 153 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 189 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP H 155 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.624A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS H 207 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS H 220 " --> pdb=" O CYS H 207 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER L 92 " --> pdb=" O VAL L 101 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.907A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE L 50 " --> pdb=" O TRP L 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 37 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 38 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR L 88 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 119 through 123 removed outlier: 4.278A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR L 177 " --> pdb=" O ASP L 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 178 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER L 170 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 135 through 136 Processing sheet with id=AG9, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.627A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR L 201 " --> pdb=" O THR L 150 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR L 196 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS L 198 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL L 200 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL L 207 " --> pdb=" O VAL L 200 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.691A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 23 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE G 52 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE G 57 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.989A pdb=" N LYS G 12 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU G 113 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 131 through 135 removed outlier: 3.589A pdb=" N SER G 131 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY G 150 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 149 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER G 191 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 153 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU G 189 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP G 155 " --> pdb=" O TYR G 187 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR G 187 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.515A pdb=" N THR G 162 " --> pdb=" O ASN G 210 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AH7, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER I 92 " --> pdb=" O VAL I 101 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 47 through 51 removed outlier: 6.834A pdb=" N LEU I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLN I 39 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE I 50 " --> pdb=" O TRP I 37 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP I 37 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR I 88 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.990A pdb=" N PHE I 123 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR I 177 " --> pdb=" O ASP I 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 178 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 170 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 135 through 136 Processing sheet with id=AI2, first strand: chain 'I' and resid 159 through 160 removed outlier: 4.554A pdb=" N TRP I 153 " --> pdb=" O VAL I 160 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR I 150 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR I 201 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR I 196 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS I 198 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS I 209 " --> pdb=" O CYS I 198 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL I 200 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL I 207 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.546A pdb=" N SER D 73 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 68 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.631A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 9 through 11 removed outlier: 6.631A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.718A pdb=" N PHE D 129 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 164 through 166 removed outlier: 4.080A pdb=" N TRP D 159 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 215 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AJ1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.742A pdb=" N VAL E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 59 through 61 removed outlier: 5.070A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 51 " --> pdb=" O TRP E 38 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 127 through 131 removed outlier: 3.638A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR E 183 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.240A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AJ8, first strand: chain 'K' and resid 9 through 11 removed outlier: 6.849A pdb=" N VAL K 10 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'K' and resid 125 through 129 removed outlier: 3.510A pdb=" N PHE K 129 " --> pdb=" O VAL K 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL K 144 " --> pdb=" O PHE K 129 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR K 183 " --> pdb=" O ASP K 149 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 164 through 166 removed outlier: 4.121A pdb=" N TRP K 159 " --> pdb=" O VAL K 166 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AK4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.664A pdb=" N VAL M 12 " --> pdb=" O THR M 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.926A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR M 109 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'M' and resid 59 through 61 removed outlier: 6.926A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP M 36 " --> pdb=" O CYS M 52 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'M' and resid 127 through 131 removed outlier: 3.651A pdb=" N GLY M 146 " --> pdb=" O LEU M 131 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR M 183 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'M' and resid 158 through 161 removed outlier: 4.228A pdb=" N TYR M 201 " --> pdb=" O VAL M 218 " (cutoff:3.500A) 1381 hydrogen bonds defined for protein. 3624 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: 11.84 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12291 1.34 - 1.46: 9543 1.46 - 1.58: 17646 1.58 - 1.71: 0 1.71 - 1.83: 194 Bond restraints: 39674 Sorted by residual: bond pdb=" N ILE B 326 " pdb=" CA ILE B 326 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.13e+01 bond pdb=" N VAL B 539 " pdb=" CA VAL B 539 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.15e-02 7.56e+03 9.59e+00 bond pdb=" N ALA B 520 " pdb=" CA ALA B 520 " ideal model delta sigma weight residual 1.453 1.482 -0.028 9.20e-03 1.18e+04 9.42e+00 bond pdb=" N VAL B 395 " pdb=" CA VAL B 395 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.37e+00 ... (remaining 39669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 52861 1.83 - 3.65: 1050 3.65 - 5.48: 88 5.48 - 7.31: 36 7.31 - 9.13: 12 Bond angle restraints: 54047 Sorted by residual: angle pdb=" O GLY C 526 " pdb=" C GLY C 526 " pdb=" N PRO C 527 " ideal model delta sigma weight residual 121.77 113.77 8.00 1.00e+00 1.00e+00 6.40e+01 angle pdb=" C THR B 333 " pdb=" CA THR B 333 " pdb=" CB THR B 333 " ideal model delta sigma weight residual 109.48 116.88 -7.40 1.68e+00 3.54e-01 1.94e+01 angle pdb=" N ASN B 331 " pdb=" CA ASN B 331 " pdb=" C ASN B 331 " ideal model delta sigma weight residual 113.18 107.66 5.52 1.33e+00 5.65e-01 1.72e+01 angle pdb=" CA LYS C 558 " pdb=" CB LYS C 558 " pdb=" CG LYS C 558 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA ASN B 544 " pdb=" C ASN B 544 " pdb=" O ASN B 544 " ideal model delta sigma weight residual 122.03 117.83 4.20 1.17e+00 7.31e-01 1.29e+01 ... (remaining 54042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 21880 17.85 - 35.71: 1909 35.71 - 53.56: 500 53.56 - 71.41: 85 71.41 - 89.26: 40 Dihedral angle restraints: 24414 sinusoidal: 10087 harmonic: 14327 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -173.61 87.61 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual 93.00 5.44 87.56 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual -86.00 -171.05 85.05 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 24411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 6202 0.121 - 0.242: 88 0.242 - 0.363: 4 0.363 - 0.485: 0 0.485 - 0.606: 2 Chirality restraints: 6296 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 6293 not shown) Planarity restraints: 6948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 526 " 0.053 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C GLY C 526 " -0.175 2.00e-02 2.50e+03 pdb=" O GLY C 526 " 0.065 2.00e-02 2.50e+03 pdb=" N PRO C 527 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 526 " -0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLY B 526 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY B 526 " -0.031 2.00e-02 2.50e+03 pdb=" N PRO B 527 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 102 " 0.014 2.00e-02 2.50e+03 1.40e-02 4.89e+00 pdb=" CG TRP E 102 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 102 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 102 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 102 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 102 " 0.004 2.00e-02 2.50e+03 ... (remaining 6945 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 518 2.65 - 3.21: 32876 3.21 - 3.78: 59352 3.78 - 4.34: 78229 4.34 - 4.90: 130212 Nonbonded interactions: 301187 Sorted by model distance: nonbonded pdb=" OG1 THR B 430 " pdb=" O ARG C 983 " model vdw 2.091 3.040 nonbonded pdb=" OG SER M 7 " pdb=" OG1 THR M 21 " model vdw 2.249 3.040 nonbonded pdb=" OG SER K 28 " pdb=" OG SER K 31 " model vdw 2.250 3.040 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR C 333 " pdb=" OD2 ASP C 364 " model vdw 2.252 3.040 ... (remaining 301182 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.510 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.004 0.048 39789 Z= 0.200 Angle : 0.611 16.328 54334 Z= 0.319 Chirality : 0.047 0.606 6296 Planarity : 0.005 0.101 6903 Dihedral : 14.268 89.263 15056 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.73 % Allowed : 18.23 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.12), residues: 4894 helix: 0.68 (0.20), residues: 645 sheet: 0.11 (0.15), residues: 1289 loop : -1.61 (0.10), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 106 TYR 0.028 0.001 TYR E 54 PHE 0.020 0.001 PHE B 133 TRP 0.037 0.001 TRP E 102 HIS 0.003 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00350 (39674) covalent geometry : angle 0.58534 (54047) SS BOND : bond 0.00137 ( 58) SS BOND : angle 0.78328 ( 116) hydrogen bonds : bond 0.24742 ( 1263) hydrogen bonds : angle 8.94698 ( 3624) link_BETA1-4 : bond 0.00542 ( 12) link_BETA1-4 : angle 1.04598 ( 36) link_NAG-ASN : bond 0.00697 ( 45) link_NAG-ASN : angle 3.50104 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 447 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 106 PHE cc_start: 0.7029 (m-80) cc_final: 0.6611 (m-80) REVERT: A 153 MET cc_start: 0.6591 (tmm) cc_final: 0.5378 (pmm) REVERT: A 237 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8619 (ttp-110) REVERT: A 464 PHE cc_start: 0.6142 (m-80) cc_final: 0.5845 (t80) REVERT: A 699 LEU cc_start: 0.8833 (mt) cc_final: 0.8564 (mt) REVERT: A 727 LEU cc_start: 0.9287 (mt) cc_final: 0.9068 (mt) REVERT: A 753 LEU cc_start: 0.8528 (mt) cc_final: 0.8304 (tp) REVERT: A 774 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8712 (tp40) REVERT: A 869 MET cc_start: 0.9057 (mtm) cc_final: 0.8784 (mtt) REVERT: A 1006 THR cc_start: 0.9020 (m) cc_final: 0.8782 (m) REVERT: B 88 ASP cc_start: 0.6984 (p0) cc_final: 0.6766 (p0) REVERT: B 117 LEU cc_start: 0.9015 (mp) cc_final: 0.8785 (tp) REVERT: B 153 MET cc_start: 0.7317 (tmm) cc_final: 0.5815 (pmm) REVERT: B 198 ASP cc_start: 0.8176 (m-30) cc_final: 0.7570 (m-30) REVERT: B 393 THR cc_start: 0.5130 (OUTLIER) cc_final: 0.4664 (p) REVERT: B 805 ILE cc_start: 0.9303 (pt) cc_final: 0.8837 (mt) REVERT: B 867 ASP cc_start: 0.8612 (m-30) cc_final: 0.8392 (p0) REVERT: B 902 MET cc_start: 0.8954 (tpp) cc_final: 0.8715 (tpt) REVERT: B 957 GLN cc_start: 0.8434 (pt0) cc_final: 0.7914 (pp30) REVERT: B 997 ILE cc_start: 0.9675 (mm) cc_final: 0.9377 (mm) REVERT: C 201 PHE cc_start: 0.7641 (t80) cc_final: 0.6467 (t80) REVERT: C 228 ASP cc_start: 0.6620 (t0) cc_final: 0.6193 (t0) REVERT: C 768 THR cc_start: 0.8978 (m) cc_final: 0.8729 (p) REVERT: C 773 GLU cc_start: 0.8728 (tt0) cc_final: 0.8490 (tp30) REVERT: C 900 MET cc_start: 0.8917 (mtp) cc_final: 0.8318 (mtm) REVERT: C 947 LYS cc_start: 0.9004 (mppt) cc_final: 0.8749 (mmtp) REVERT: C 969 ASN cc_start: 0.9192 (m-40) cc_final: 0.8758 (p0) REVERT: C 1008 VAL cc_start: 0.9560 (t) cc_final: 0.9118 (p) REVERT: C 1055 SER cc_start: 0.9461 (t) cc_final: 0.9168 (m) REVERT: H 80 TYR cc_start: 0.6935 (m-80) cc_final: 0.6652 (m-10) REVERT: L 134 LYS cc_start: -0.1457 (pttt) cc_final: -0.1802 (tttt) REVERT: G 59 ASN cc_start: 0.6410 (t0) cc_final: 0.6120 (m-40) REVERT: G 73 ASP cc_start: 0.6426 (m-30) cc_final: 0.5799 (t0) REVERT: D 107 LEU cc_start: 0.3280 (tp) cc_final: 0.2865 (tt) REVERT: E 48 GLU cc_start: 0.6999 (tt0) cc_final: 0.6784 (tp30) REVERT: K 51 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6389 (mt-10) REVERT: K 63 PHE cc_start: 0.1041 (m-80) cc_final: 0.0185 (m-10) outliers start: 31 outliers final: 7 residues processed: 470 average time/residue: 0.2443 time to fit residues: 183.4279 Evaluate side-chains 223 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 613 GLN B 913 GLN B1005 GLN C 66 HIS C 439 ASN C 506 GLN C 762 GLN C 895 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 HIS I 113 GLN I 202 HIS D 38 GLN K 72 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.144440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.108995 restraints weight = 147215.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.107250 restraints weight = 145931.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.105839 restraints weight = 111470.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.103995 restraints weight = 120199.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.104421 restraints weight = 104915.425| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 39789 Z= 0.280 Angle : 0.714 14.551 54334 Z= 0.361 Chirality : 0.047 0.469 6296 Planarity : 0.005 0.087 6903 Dihedral : 6.025 59.408 6505 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 3.44 % Allowed : 17.99 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.12), residues: 4894 helix: 0.92 (0.20), residues: 705 sheet: 0.04 (0.14), residues: 1441 loop : -1.66 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 765 TYR 0.037 0.002 TYR K 151 PHE 0.029 0.002 PHE H 177 TRP 0.023 0.002 TRP D 36 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00631 (39674) covalent geometry : angle 0.69218 (54047) SS BOND : bond 0.00401 ( 58) SS BOND : angle 1.56110 ( 116) hydrogen bonds : bond 0.04382 ( 1263) hydrogen bonds : angle 6.27766 ( 3624) link_BETA1-4 : bond 0.00362 ( 12) link_BETA1-4 : angle 1.25505 ( 36) link_NAG-ASN : bond 0.00743 ( 45) link_NAG-ASN : angle 3.32842 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 223 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5359 (OUTLIER) cc_final: 0.4880 (m-80) REVERT: A 153 MET cc_start: 0.6102 (tmm) cc_final: 0.5192 (pmm) REVERT: A 461 LEU cc_start: -0.3184 (OUTLIER) cc_final: -0.4915 (mt) REVERT: A 699 LEU cc_start: 0.9034 (mt) cc_final: 0.7351 (mt) REVERT: B 153 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.5293 (pmm) REVERT: B 202 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8852 (mmtm) REVERT: B 388 ASN cc_start: 0.0803 (OUTLIER) cc_final: 0.0154 (m110) REVERT: B 391 CYS cc_start: 0.0053 (OUTLIER) cc_final: -0.0598 (m) REVERT: B 670 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8677 (mm) REVERT: B 902 MET cc_start: 0.9412 (tpp) cc_final: 0.8901 (tpp) REVERT: B 957 GLN cc_start: 0.8450 (pt0) cc_final: 0.8024 (pp30) REVERT: B 969 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8021 (m-40) REVERT: B 1086 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7689 (pttm) REVERT: C 201 PHE cc_start: 0.7419 (t80) cc_final: 0.6983 (t80) REVERT: C 342 PHE cc_start: 0.4807 (m-10) cc_final: 0.4160 (t80) REVERT: C 562 PHE cc_start: 0.7443 (p90) cc_final: 0.7141 (p90) REVERT: C 565 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7438 (m-10) REVERT: C 786 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7743 (ptpp) REVERT: C 878 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9228 (mp) REVERT: C 900 MET cc_start: 0.8832 (mtp) cc_final: 0.8297 (mtm) REVERT: C 947 LYS cc_start: 0.9061 (mppt) cc_final: 0.8853 (mmtp) REVERT: C 1008 VAL cc_start: 0.9610 (t) cc_final: 0.9279 (p) REVERT: H 6 GLU cc_start: 0.4342 (OUTLIER) cc_final: 0.1840 (mp0) REVERT: G 46 GLU cc_start: 0.5375 (pt0) cc_final: 0.5125 (mm-30) REVERT: E 34 TYR cc_start: 0.4339 (t80) cc_final: 0.3515 (t80) REVERT: E 119 SER cc_start: 0.2747 (OUTLIER) cc_final: 0.2450 (p) REVERT: E 147 CYS cc_start: 0.0600 (OUTLIER) cc_final: 0.0186 (p) REVERT: K 57 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.6694 (t) REVERT: K 121 LYS cc_start: 0.2534 (OUTLIER) cc_final: 0.1256 (mppt) outliers start: 147 outliers final: 52 residues processed: 350 average time/residue: 0.2157 time to fit residues: 129.0294 Evaluate side-chains 224 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 157 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain M residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 315 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 chunk 311 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN K 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.144499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.108136 restraints weight = 145872.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.106502 restraints weight = 130877.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.105365 restraints weight = 94286.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.104008 restraints weight = 87910.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104275 restraints weight = 97162.374| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39789 Z= 0.170 Angle : 0.589 12.983 54334 Z= 0.294 Chirality : 0.045 0.491 6296 Planarity : 0.004 0.086 6903 Dihedral : 5.421 57.116 6493 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 2.79 % Allowed : 18.96 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.12), residues: 4894 helix: 1.36 (0.21), residues: 697 sheet: 0.05 (0.14), residues: 1403 loop : -1.53 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.020 0.001 TYR A 508 PHE 0.018 0.001 PHE M 35 TRP 0.022 0.001 TRP D 36 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00387 (39674) covalent geometry : angle 0.56374 (54047) SS BOND : bond 0.00298 ( 58) SS BOND : angle 1.51154 ( 116) hydrogen bonds : bond 0.03868 ( 1263) hydrogen bonds : angle 5.80787 ( 3624) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 0.89746 ( 36) link_NAG-ASN : bond 0.00627 ( 45) link_NAG-ASN : angle 3.16568 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 186 time to evaluate : 1.465 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 91 TYR cc_start: 0.8684 (t80) cc_final: 0.8432 (t80) REVERT: A 133 PHE cc_start: 0.5316 (OUTLIER) cc_final: 0.4922 (m-80) REVERT: A 153 MET cc_start: 0.5986 (tmm) cc_final: 0.5037 (pmm) REVERT: A 191 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6130 (mm-30) REVERT: A 461 LEU cc_start: -0.3044 (OUTLIER) cc_final: -0.4759 (mt) REVERT: A 699 LEU cc_start: 0.8835 (mt) cc_final: 0.8500 (mt) REVERT: A 873 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: B 153 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.5272 (pmm) REVERT: B 703 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8160 (p0) REVERT: B 780 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7983 (tt0) REVERT: B 873 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.8967 (m-10) REVERT: B 957 GLN cc_start: 0.8304 (pt0) cc_final: 0.7964 (pp30) REVERT: B 969 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8073 (m-40) REVERT: B 1086 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7681 (pttm) REVERT: C 189 LEU cc_start: 0.8466 (pp) cc_final: 0.8248 (pp) REVERT: C 201 PHE cc_start: 0.7561 (t80) cc_final: 0.7244 (t80) REVERT: C 565 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: C 786 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7759 (ptpt) REVERT: C 878 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9127 (mp) REVERT: C 900 MET cc_start: 0.8903 (mtp) cc_final: 0.8375 (mtm) REVERT: C 947 LYS cc_start: 0.8955 (mppt) cc_final: 0.8753 (mmtp) REVERT: C 1008 VAL cc_start: 0.9563 (t) cc_final: 0.9282 (p) REVERT: C 1104 VAL cc_start: 0.9746 (OUTLIER) cc_final: 0.9544 (p) REVERT: H 6 GLU cc_start: 0.3358 (OUTLIER) cc_final: 0.1739 (mp0) REVERT: G 46 GLU cc_start: 0.5361 (pt0) cc_final: 0.5015 (mm-30) REVERT: E 34 TYR cc_start: 0.4669 (t80) cc_final: 0.4322 (t80) REVERT: E 115 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4894 (mp) REVERT: E 119 SER cc_start: 0.2200 (OUTLIER) cc_final: 0.1470 (p) REVERT: E 147 CYS cc_start: 0.0332 (OUTLIER) cc_final: -0.0148 (m) REVERT: K 3 MET cc_start: 0.7235 (tpp) cc_final: 0.6936 (mmm) REVERT: K 121 LYS cc_start: 0.2423 (OUTLIER) cc_final: 0.1156 (mppt) outliers start: 119 outliers final: 65 residues processed: 291 average time/residue: 0.2026 time to fit residues: 99.6017 Evaluate side-chains 237 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 537 LYS Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 123 optimal weight: 9.9990 chunk 475 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 460 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 370 optimal weight: 30.0000 chunk 424 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 211 ASN B 388 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 498 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN E 3 GLN M 204 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.140282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094556 restraints weight = 145739.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.090085 restraints weight = 101934.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.090600 restraints weight = 90160.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090687 restraints weight = 78320.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090759 restraints weight = 74680.829| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 39789 Z= 0.324 Angle : 0.753 13.854 54334 Z= 0.377 Chirality : 0.049 0.439 6296 Planarity : 0.005 0.080 6903 Dihedral : 6.019 59.844 6493 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 4.43 % Allowed : 18.72 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.12), residues: 4894 helix: 0.85 (0.20), residues: 695 sheet: -0.26 (0.13), residues: 1439 loop : -1.58 (0.11), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 99 TYR 0.023 0.002 TYR B 904 PHE 0.023 0.002 PHE B 392 TRP 0.038 0.002 TRP I 37 HIS 0.013 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00728 (39674) covalent geometry : angle 0.73075 (54047) SS BOND : bond 0.01127 ( 58) SS BOND : angle 1.81540 ( 116) hydrogen bonds : bond 0.04270 ( 1263) hydrogen bonds : angle 5.92031 ( 3624) link_BETA1-4 : bond 0.00505 ( 12) link_BETA1-4 : angle 1.35467 ( 36) link_NAG-ASN : bond 0.00876 ( 45) link_NAG-ASN : angle 3.30944 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 168 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9084 (mm) REVERT: A 133 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.5856 (m-80) REVERT: A 153 MET cc_start: 0.4939 (tmm) cc_final: 0.3873 (pmm) REVERT: A 191 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6621 (mm-30) REVERT: A 238 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7764 (p90) REVERT: A 461 LEU cc_start: -0.1582 (OUTLIER) cc_final: -0.4333 (mt) REVERT: A 1130 ILE cc_start: 0.8169 (pt) cc_final: 0.7938 (tt) REVERT: B 88 ASP cc_start: 0.7304 (p0) cc_final: 0.7040 (p0) REVERT: B 153 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.5730 (pmm) REVERT: B 347 PHE cc_start: -0.0108 (OUTLIER) cc_final: -0.1808 (t80) REVERT: B 703 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8332 (p0) REVERT: B 780 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8270 (tt0) REVERT: B 902 MET cc_start: 0.9350 (tpp) cc_final: 0.9061 (tpp) REVERT: B 957 GLN cc_start: 0.8753 (pt0) cc_final: 0.8380 (pp30) REVERT: B 962 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8985 (tp) REVERT: B 969 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8340 (m-40) REVERT: C 201 PHE cc_start: 0.8292 (t80) cc_final: 0.7870 (t80) REVERT: C 518 LEU cc_start: 0.3463 (OUTLIER) cc_final: 0.2474 (mt) REVERT: C 592 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: C 703 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8857 (p0) REVERT: C 900 MET cc_start: 0.8876 (mtp) cc_final: 0.8446 (mtm) REVERT: E 3 GLN cc_start: 0.4314 (OUTLIER) cc_final: 0.4098 (pp30) REVERT: E 75 THR cc_start: 0.4906 (OUTLIER) cc_final: 0.4520 (p) REVERT: E 112 GLN cc_start: 0.5135 (pm20) cc_final: 0.3439 (mm110) REVERT: E 115 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5140 (mp) REVERT: E 119 SER cc_start: 0.2815 (OUTLIER) cc_final: 0.1855 (p) REVERT: E 147 CYS cc_start: 0.2519 (p) cc_final: 0.1931 (m) REVERT: K 57 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7149 (t) REVERT: K 121 LYS cc_start: 0.3249 (OUTLIER) cc_final: 0.2291 (mmtt) outliers start: 189 outliers final: 98 residues processed: 337 average time/residue: 0.1996 time to fit residues: 115.0132 Evaluate side-chains 251 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 135 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 267 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 300 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 chunk 407 optimal weight: 40.0000 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 335 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 992 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.142846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.106617 restraints weight = 143855.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.104842 restraints weight = 130090.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.103038 restraints weight = 96432.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.102498 restraints weight = 78867.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102503 restraints weight = 83666.277| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39789 Z= 0.111 Angle : 0.559 14.090 54334 Z= 0.277 Chirality : 0.045 0.446 6296 Planarity : 0.004 0.073 6903 Dihedral : 5.285 59.416 6489 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 2.39 % Allowed : 20.88 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.12), residues: 4894 helix: 1.44 (0.20), residues: 696 sheet: -0.08 (0.13), residues: 1427 loop : -1.45 (0.11), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.015 0.001 TYR K 151 PHE 0.025 0.001 PHE B 329 TRP 0.010 0.001 TRP E 110 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00245 (39674) covalent geometry : angle 0.53877 (54047) SS BOND : bond 0.00261 ( 58) SS BOND : angle 1.40815 ( 116) hydrogen bonds : bond 0.03284 ( 1263) hydrogen bonds : angle 5.35633 ( 3624) link_BETA1-4 : bond 0.00435 ( 12) link_BETA1-4 : angle 0.86346 ( 36) link_NAG-ASN : bond 0.00555 ( 45) link_NAG-ASN : angle 2.79609 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 165 time to evaluate : 1.375 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 153 MET cc_start: 0.4669 (tmm) cc_final: 0.4123 (pmm) REVERT: A 191 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6429 (mm-30) REVERT: A 237 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8392 (ttp-110) REVERT: A 461 LEU cc_start: -0.3693 (OUTLIER) cc_final: -0.5326 (mt) REVERT: A 873 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.8870 (m-80) REVERT: B 153 MET cc_start: 0.6605 (tmm) cc_final: 0.5228 (pmm) REVERT: B 347 PHE cc_start: 0.0209 (OUTLIER) cc_final: -0.1462 (t80) REVERT: B 703 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8456 (p0) REVERT: B 957 GLN cc_start: 0.8352 (pt0) cc_final: 0.8126 (pp30) REVERT: B 1008 VAL cc_start: 0.9753 (t) cc_final: 0.9515 (p) REVERT: C 376 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 518 LEU cc_start: 0.3214 (OUTLIER) cc_final: 0.1999 (mt) REVERT: C 697 MET cc_start: 0.8293 (ttm) cc_final: 0.7966 (ttt) REVERT: C 900 MET cc_start: 0.8945 (mtp) cc_final: 0.8694 (mtm) REVERT: H 13 LYS cc_start: 0.5710 (tptp) cc_final: 0.5501 (tptp) REVERT: E 68 ARG cc_start: 0.4469 (ptp-170) cc_final: 0.3405 (ptp-170) REVERT: E 112 GLN cc_start: 0.4846 (pm20) cc_final: 0.2791 (mm110) REVERT: E 119 SER cc_start: 0.1699 (OUTLIER) cc_final: 0.0424 (p) outliers start: 102 outliers final: 61 residues processed: 249 average time/residue: 0.2112 time to fit residues: 90.4295 Evaluate side-chains 209 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 450 optimal weight: 50.0000 chunk 240 optimal weight: 4.9990 chunk 326 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 542 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 544 ASN C 99 ASN C 207 HIS C 460 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.138851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.104127 restraints weight = 144802.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.101628 restraints weight = 183957.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098767 restraints weight = 141424.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097408 restraints weight = 163301.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097816 restraints weight = 127698.018| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 39789 Z= 0.350 Angle : 0.765 14.199 54334 Z= 0.380 Chirality : 0.049 0.404 6296 Planarity : 0.005 0.074 6903 Dihedral : 5.867 57.193 6485 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.91 % Favored : 94.07 % Rotamer: Outliers : 3.80 % Allowed : 20.43 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.12), residues: 4894 helix: 0.88 (0.20), residues: 706 sheet: -0.32 (0.13), residues: 1424 loop : -1.55 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1107 TYR 0.035 0.002 TYR E 34 PHE 0.029 0.002 PHE B 329 TRP 0.035 0.002 TRP I 37 HIS 0.014 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00788 (39674) covalent geometry : angle 0.74450 (54047) SS BOND : bond 0.00434 ( 58) SS BOND : angle 1.86747 ( 116) hydrogen bonds : bond 0.04147 ( 1263) hydrogen bonds : angle 5.84631 ( 3624) link_BETA1-4 : bond 0.00581 ( 12) link_BETA1-4 : angle 1.43017 ( 36) link_NAG-ASN : bond 0.00896 ( 45) link_NAG-ASN : angle 3.22198 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 144 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6501 (mm-30) REVERT: A 238 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7701 (p90) REVERT: A 461 LEU cc_start: -0.2713 (OUTLIER) cc_final: -0.4709 (mt) REVERT: A 532 ASN cc_start: 0.8630 (t0) cc_final: 0.8407 (t0) REVERT: A 873 TYR cc_start: 0.9407 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: A 962 LEU cc_start: 0.9469 (tp) cc_final: 0.9208 (tp) REVERT: B 153 MET cc_start: 0.6072 (OUTLIER) cc_final: 0.4834 (pmm) REVERT: B 347 PHE cc_start: 0.0842 (OUTLIER) cc_final: -0.1452 (t80) REVERT: B 703 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8349 (p0) REVERT: B 869 MET cc_start: 0.8737 (tpp) cc_final: 0.8484 (tpp) REVERT: B 902 MET cc_start: 0.9431 (tpp) cc_final: 0.8945 (tpt) REVERT: B 957 GLN cc_start: 0.8717 (pt0) cc_final: 0.8337 (pp30) REVERT: B 980 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8703 (mm) REVERT: C 518 LEU cc_start: 0.3370 (OUTLIER) cc_final: 0.2061 (mt) REVERT: C 562 PHE cc_start: 0.8236 (p90) cc_final: 0.7962 (p90) REVERT: C 1050 MET cc_start: 0.8761 (ptp) cc_final: 0.8538 (ptp) REVERT: C 1106 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8813 (pt0) REVERT: H 70 ILE cc_start: -0.2105 (OUTLIER) cc_final: -0.2334 (mt) REVERT: E 115 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4892 (mp) outliers start: 162 outliers final: 102 residues processed: 291 average time/residue: 0.1946 time to fit residues: 99.9043 Evaluate side-chains 243 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 130 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 263 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 274 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 151 optimal weight: 40.0000 chunk 304 optimal weight: 0.9980 chunk 463 optimal weight: 9.9990 chunk 449 optimal weight: 50.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN A 901 GLN A 992 GLN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN M 3 GLN M 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.104001 restraints weight = 145164.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.101996 restraints weight = 131441.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100760 restraints weight = 95723.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100061 restraints weight = 73186.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100268 restraints weight = 88893.348| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39789 Z= 0.136 Angle : 0.585 15.951 54334 Z= 0.288 Chirality : 0.045 0.407 6296 Planarity : 0.004 0.071 6903 Dihedral : 5.378 57.686 6484 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 2.62 % Allowed : 21.39 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.12), residues: 4894 helix: 1.23 (0.20), residues: 718 sheet: -0.15 (0.13), residues: 1426 loop : -1.43 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 67 TYR 0.025 0.001 TYR B 904 PHE 0.024 0.001 PHE E 107 TRP 0.013 0.001 TRP D 36 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00306 (39674) covalent geometry : angle 0.56066 (54047) SS BOND : bond 0.00382 ( 58) SS BOND : angle 1.38392 ( 116) hydrogen bonds : bond 0.03314 ( 1263) hydrogen bonds : angle 5.39073 ( 3624) link_BETA1-4 : bond 0.00377 ( 12) link_BETA1-4 : angle 0.98808 ( 36) link_NAG-ASN : bond 0.00536 ( 45) link_NAG-ASN : angle 3.16424 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 152 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6484 (mm-30) REVERT: A 237 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8358 (ttp-110) REVERT: A 461 LEU cc_start: -0.2894 (OUTLIER) cc_final: -0.4793 (mt) REVERT: A 532 ASN cc_start: 0.8673 (t0) cc_final: 0.8422 (t0) REVERT: A 873 TYR cc_start: 0.9400 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: A 900 MET cc_start: 0.8966 (mtt) cc_final: 0.8765 (mtm) REVERT: A 962 LEU cc_start: 0.9431 (tp) cc_final: 0.9155 (tp) REVERT: B 153 MET cc_start: 0.6095 (tmm) cc_final: 0.4734 (pmm) REVERT: B 347 PHE cc_start: 0.1567 (OUTLIER) cc_final: -0.0479 (t80) REVERT: B 509 ARG cc_start: 0.3469 (ttt180) cc_final: 0.3130 (tpt170) REVERT: B 703 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (p0) REVERT: B 739 THR cc_start: 0.8489 (m) cc_final: 0.8239 (t) REVERT: B 740 MET cc_start: 0.6927 (tmm) cc_final: 0.6697 (tmm) REVERT: B 869 MET cc_start: 0.8737 (tpp) cc_final: 0.8466 (tpp) REVERT: B 902 MET cc_start: 0.9413 (tpp) cc_final: 0.9181 (tpt) REVERT: B 957 GLN cc_start: 0.8395 (pt0) cc_final: 0.8115 (pp30) REVERT: B 1008 VAL cc_start: 0.9765 (t) cc_final: 0.9546 (p) REVERT: C 299 THR cc_start: 0.9166 (m) cc_final: 0.8887 (p) REVERT: C 518 LEU cc_start: 0.3247 (OUTLIER) cc_final: 0.1975 (mt) REVERT: C 562 PHE cc_start: 0.8203 (p90) cc_final: 0.7841 (p90) REVERT: C 697 MET cc_start: 0.8154 (ttm) cc_final: 0.7846 (ttt) REVERT: C 866 THR cc_start: 0.9115 (p) cc_final: 0.8708 (p) REVERT: C 900 MET cc_start: 0.8759 (mtp) cc_final: 0.8485 (mtm) REVERT: C 1106 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: M 3 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5514 (tm-30) outliers start: 112 outliers final: 76 residues processed: 252 average time/residue: 0.1957 time to fit residues: 84.6168 Evaluate side-chains 219 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 135 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 385 optimal weight: 9.9990 chunk 271 optimal weight: 0.8980 chunk 156 optimal weight: 30.0000 chunk 422 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 401 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 376 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 462 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.139600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.102175 restraints weight = 145172.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.100128 restraints weight = 133271.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099872 restraints weight = 103239.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098523 restraints weight = 90524.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098707 restraints weight = 93095.217| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39789 Z= 0.210 Angle : 0.631 15.903 54334 Z= 0.312 Chirality : 0.046 0.412 6296 Planarity : 0.005 0.072 6903 Dihedral : 5.410 57.632 6484 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.44 % Rotamer: Outliers : 2.67 % Allowed : 21.49 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.12), residues: 4894 helix: 1.24 (0.20), residues: 706 sheet: -0.22 (0.13), residues: 1446 loop : -1.41 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 106 TYR 0.038 0.001 TYR B 145 PHE 0.041 0.002 PHE B 186 TRP 0.015 0.001 TRP D 36 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00475 (39674) covalent geometry : angle 0.60941 (54047) SS BOND : bond 0.00349 ( 58) SS BOND : angle 1.51196 ( 116) hydrogen bonds : bond 0.03444 ( 1263) hydrogen bonds : angle 5.46004 ( 3624) link_BETA1-4 : bond 0.00227 ( 12) link_BETA1-4 : angle 1.14206 ( 36) link_NAG-ASN : bond 0.00628 ( 45) link_NAG-ASN : angle 3.00147 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 146 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5937 (pmm) cc_final: 0.5632 (pmm) REVERT: A 191 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6456 (mm-30) REVERT: A 238 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7667 (p90) REVERT: A 461 LEU cc_start: -0.3490 (OUTLIER) cc_final: -0.5150 (mt) REVERT: A 532 ASN cc_start: 0.8780 (t0) cc_final: 0.8579 (t0) REVERT: A 873 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: A 962 LEU cc_start: 0.9466 (tp) cc_final: 0.9162 (tp) REVERT: B 153 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4458 (pmm) REVERT: B 347 PHE cc_start: 0.0840 (OUTLIER) cc_final: -0.1495 (t80) REVERT: B 703 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8625 (p0) REVERT: B 739 THR cc_start: 0.8444 (m) cc_final: 0.8209 (t) REVERT: B 869 MET cc_start: 0.8704 (tpp) cc_final: 0.8422 (tpp) REVERT: B 902 MET cc_start: 0.9431 (tpp) cc_final: 0.8920 (tpt) REVERT: B 957 GLN cc_start: 0.8572 (pt0) cc_final: 0.8230 (pp30) REVERT: C 299 THR cc_start: 0.9190 (m) cc_final: 0.8949 (p) REVERT: C 518 LEU cc_start: 0.3290 (OUTLIER) cc_final: 0.1996 (mt) REVERT: C 562 PHE cc_start: 0.8163 (p90) cc_final: 0.7742 (p90) REVERT: C 697 MET cc_start: 0.8204 (ttm) cc_final: 0.7904 (ttt) REVERT: C 900 MET cc_start: 0.8744 (mtp) cc_final: 0.8463 (mtm) REVERT: C 1106 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8760 (pt0) REVERT: E 112 GLN cc_start: 0.2704 (pm20) cc_final: 0.0977 (mm110) outliers start: 114 outliers final: 94 residues processed: 250 average time/residue: 0.1898 time to fit residues: 82.9287 Evaluate side-chains 240 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 138 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 259 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 422 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 367 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 137 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.139678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104378 restraints weight = 145339.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.102345 restraints weight = 154845.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.101749 restraints weight = 123360.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101067 restraints weight = 94149.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.101175 restraints weight = 89308.331| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39789 Z= 0.185 Angle : 0.608 15.762 54334 Z= 0.299 Chirality : 0.045 0.414 6296 Planarity : 0.004 0.073 6903 Dihedral : 5.270 57.939 6484 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.78 % Favored : 95.20 % Rotamer: Outliers : 2.74 % Allowed : 21.60 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.12), residues: 4894 helix: 1.25 (0.20), residues: 718 sheet: -0.23 (0.13), residues: 1447 loop : -1.37 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 106 TYR 0.022 0.001 TYR B 145 PHE 0.024 0.002 PHE B 186 TRP 0.047 0.001 TRP C 152 HIS 0.008 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00419 (39674) covalent geometry : angle 0.58766 (54047) SS BOND : bond 0.00491 ( 58) SS BOND : angle 1.38535 ( 116) hydrogen bonds : bond 0.03335 ( 1263) hydrogen bonds : angle 5.37667 ( 3624) link_BETA1-4 : bond 0.00346 ( 12) link_BETA1-4 : angle 1.09682 ( 36) link_NAG-ASN : bond 0.00578 ( 45) link_NAG-ASN : angle 2.91972 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 139 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5793 (pmm) cc_final: 0.5480 (pmm) REVERT: A 191 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6457 (mm-30) REVERT: A 461 LEU cc_start: -0.3032 (OUTLIER) cc_final: -0.4692 (mt) REVERT: A 873 TYR cc_start: 0.9420 (OUTLIER) cc_final: 0.8822 (m-80) REVERT: A 962 LEU cc_start: 0.9465 (tp) cc_final: 0.9168 (tp) REVERT: B 153 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.4381 (pmm) REVERT: B 347 PHE cc_start: 0.1234 (OUTLIER) cc_final: -0.0432 (t80) REVERT: B 509 ARG cc_start: 0.4066 (ttt180) cc_final: 0.3586 (tpt170) REVERT: B 703 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8538 (p0) REVERT: B 739 THR cc_start: 0.8561 (m) cc_final: 0.8333 (t) REVERT: B 902 MET cc_start: 0.9394 (tpp) cc_final: 0.8854 (tpt) REVERT: B 957 GLN cc_start: 0.8449 (pt0) cc_final: 0.8132 (pp30) REVERT: B 1086 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7877 (pttp) REVERT: B 1107 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8003 (mtt90) REVERT: C 299 THR cc_start: 0.9170 (m) cc_final: 0.8966 (p) REVERT: C 518 LEU cc_start: 0.3468 (OUTLIER) cc_final: 0.2055 (mt) REVERT: C 562 PHE cc_start: 0.8017 (p90) cc_final: 0.7781 (p90) REVERT: C 596 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8726 (p) REVERT: C 697 MET cc_start: 0.8188 (ttm) cc_final: 0.7890 (ttt) REVERT: C 858 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (pt) REVERT: C 866 THR cc_start: 0.9166 (p) cc_final: 0.8768 (p) REVERT: C 900 MET cc_start: 0.8899 (mtp) cc_final: 0.8492 (mtm) REVERT: C 1106 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: E 112 GLN cc_start: 0.2720 (pm20) cc_final: 0.0955 (mm110) REVERT: M 115 LEU cc_start: 0.7077 (pp) cc_final: 0.6639 (mm) outliers start: 117 outliers final: 90 residues processed: 248 average time/residue: 0.1890 time to fit residues: 83.6659 Evaluate side-chains 234 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 133 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 210 ASN Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 375 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 chunk 164 optimal weight: 0.9980 chunk 420 optimal weight: 0.2980 chunk 305 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 418 optimal weight: 8.9990 chunk 3 optimal weight: 0.0980 chunk 256 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.141330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.103762 restraints weight = 145103.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.101100 restraints weight = 146484.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101809 restraints weight = 103373.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.101129 restraints weight = 79204.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101218 restraints weight = 78707.500| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39789 Z= 0.101 Angle : 0.558 16.282 54334 Z= 0.273 Chirality : 0.045 0.383 6296 Planarity : 0.004 0.071 6903 Dihedral : 4.868 58.061 6484 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 1.87 % Allowed : 22.56 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.12), residues: 4894 helix: 1.59 (0.21), residues: 688 sheet: -0.19 (0.14), residues: 1427 loop : -1.24 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 106 TYR 0.020 0.001 TYR G 80 PHE 0.031 0.001 PHE B 133 TRP 0.038 0.001 TRP C 152 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00227 (39674) covalent geometry : angle 0.53999 (54047) SS BOND : bond 0.00314 ( 58) SS BOND : angle 1.14078 ( 116) hydrogen bonds : bond 0.02995 ( 1263) hydrogen bonds : angle 5.11460 ( 3624) link_BETA1-4 : bond 0.00381 ( 12) link_BETA1-4 : angle 0.79717 ( 36) link_NAG-ASN : bond 0.00522 ( 45) link_NAG-ASN : angle 2.68691 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 159 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5971 (pmm) cc_final: 0.5580 (pmm) REVERT: A 191 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6451 (mm-30) REVERT: A 461 LEU cc_start: -0.3205 (OUTLIER) cc_final: -0.4856 (mt) REVERT: A 873 TYR cc_start: 0.9421 (OUTLIER) cc_final: 0.8818 (m-80) REVERT: A 900 MET cc_start: 0.8717 (mtt) cc_final: 0.8436 (mtm) REVERT: A 962 LEU cc_start: 0.9434 (tp) cc_final: 0.9118 (tp) REVERT: B 153 MET cc_start: 0.6025 (tmm) cc_final: 0.4747 (pmm) REVERT: B 347 PHE cc_start: 0.0827 (OUTLIER) cc_final: -0.0806 (t80) REVERT: B 509 ARG cc_start: 0.4037 (ttt180) cc_final: 0.3662 (tpt170) REVERT: B 739 THR cc_start: 0.8290 (m) cc_final: 0.8089 (t) REVERT: B 902 MET cc_start: 0.9380 (tpp) cc_final: 0.9113 (tpt) REVERT: B 957 GLN cc_start: 0.8413 (pt0) cc_final: 0.8117 (pp30) REVERT: C 518 LEU cc_start: 0.3377 (OUTLIER) cc_final: 0.2296 (mp) REVERT: C 562 PHE cc_start: 0.8175 (p90) cc_final: 0.7863 (p90) REVERT: C 596 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8655 (p) REVERT: C 697 MET cc_start: 0.8197 (ttm) cc_final: 0.7899 (ttt) REVERT: C 900 MET cc_start: 0.8735 (mtp) cc_final: 0.8466 (mtm) REVERT: C 1106 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: H 137 PRO cc_start: 0.4934 (Cg_exo) cc_final: 0.4603 (Cg_endo) REVERT: L 154 LYS cc_start: 0.2892 (mptt) cc_final: 0.1591 (pttt) REVERT: E 112 GLN cc_start: 0.2613 (pm20) cc_final: 0.0917 (mm110) REVERT: E 115 LEU cc_start: 0.5832 (tp) cc_final: 0.5407 (mp) REVERT: E 147 CYS cc_start: 0.0665 (m) cc_final: 0.0120 (p) REVERT: M 115 LEU cc_start: 0.7054 (pp) cc_final: 0.6612 (mm) outliers start: 80 outliers final: 65 residues processed: 232 average time/residue: 0.2029 time to fit residues: 83.2981 Evaluate side-chains 219 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 142 THR Chi-restraints excluded: chain M residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 260 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 381 optimal weight: 50.0000 chunk 441 optimal weight: 40.0000 chunk 163 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.101516 restraints weight = 144883.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.099420 restraints weight = 141959.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.097092 restraints weight = 106823.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.096325 restraints weight = 89319.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096469 restraints weight = 93319.131| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 39789 Z= 0.246 Angle : 0.669 15.922 54334 Z= 0.330 Chirality : 0.046 0.400 6296 Planarity : 0.005 0.091 6903 Dihedral : 5.240 58.126 6484 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer: Outliers : 2.32 % Allowed : 22.40 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.12), residues: 4894 helix: 1.22 (0.20), residues: 699 sheet: -0.18 (0.14), residues: 1427 loop : -1.35 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1107 TYR 0.036 0.002 TYR K 183 PHE 0.022 0.002 PHE B 92 TRP 0.052 0.002 TRP C 152 HIS 0.010 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00552 (39674) covalent geometry : angle 0.64968 (54047) SS BOND : bond 0.00383 ( 58) SS BOND : angle 1.59833 ( 116) hydrogen bonds : bond 0.03597 ( 1263) hydrogen bonds : angle 5.43756 ( 3624) link_BETA1-4 : bond 0.00247 ( 12) link_BETA1-4 : angle 1.30478 ( 36) link_NAG-ASN : bond 0.00693 ( 45) link_NAG-ASN : angle 2.94229 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6182.76 seconds wall clock time: 108 minutes 7.14 seconds (6487.14 seconds total)