Starting phenix.real_space_refine on Thu Dec 26 09:38:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_60107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_60107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_60107.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_60107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhl_60107/12_2024/8zhl_60107.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 22.25, per 1000 atoms: 0.57 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: 9.79 Conformation dependent library (CDL) restraints added in 5.1 seconds 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: 6.81 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: 22.81 Time building geometry restraints manager: 11.36 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: 0.00 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.060 Extract box with map and model: 1.540 Check model and map are aligned: 0.300 Set scattering table: 0.340 Process input model: 94.070 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.990 ------------------------------------------------------------------------------- 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 : 0.003 0.048 39674 Z= 0.229 Angle : 0.585 9.132 54047 Z= 0.314 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), 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 TRP 0.037 0.001 TRP E 102 HIS 0.003 0.001 HIS G 211 PHE 0.020 0.001 PHE B 133 TYR 0.028 0.001 TYR E 54 ARG 0.009 0.000 ARG M 106 *********************** 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 : 4.558 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: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6591 (tmm) cc_final: 0.5379 (pmm) REVERT: A 237 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8538 (ttp-110) REVERT: A 464 PHE cc_start: 0.6142 (m-80) cc_final: 0.5847 (t80) REVERT: A 699 LEU cc_start: 0.8833 (mt) cc_final: 0.7620 (mt) REVERT: A 727 LEU cc_start: 0.9287 (mt) cc_final: 0.9070 (mt) REVERT: A 753 LEU cc_start: 0.8528 (mt) cc_final: 0.8305 (tp) REVERT: A 869 MET cc_start: 0.9057 (mtm) cc_final: 0.8781 (mtt) REVERT: A 1006 THR cc_start: 0.9020 (m) cc_final: 0.8791 (m) REVERT: B 88 ASP cc_start: 0.6984 (p0) cc_final: 0.6761 (p0) REVERT: B 117 LEU cc_start: 0.9015 (mp) cc_final: 0.8787 (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: 0.7566 (m-30) REVERT: B 393 THR cc_start: 0.5130 (OUTLIER) cc_final: 0.4658 (p) REVERT: B 805 ILE cc_start: 0.9303 (pt) cc_final: 0.8838 (mt) REVERT: B 867 ASP cc_start: 0.8612 (m-30) cc_final: 0.8392 (p0) REVERT: B 869 MET cc_start: 0.8962 (mtt) cc_final: 0.8650 (mmm) REVERT: B 902 MET cc_start: 0.8954 (tpp) cc_final: 0.8717 (tpt) REVERT: B 957 GLN cc_start: 0.8434 (pt0) cc_final: 0.7933 (pp30) REVERT: B 997 ILE cc_start: 0.9675 (mm) cc_final: 0.9376 (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: 0.8728 (p) REVERT: C 773 GLU cc_start: 0.8728 (tt0) cc_final: 0.8489 (tp30) REVERT: C 947 LYS cc_start: 0.9004 (mppt) cc_final: 0.8748 (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: -0.1809 (tttt) REVERT: G 59 ASN cc_start: 0.6410 (t0) cc_final: 0.6119 (m-40) REVERT: G 73 ASP cc_start: 0.6426 (m-30) cc_final: 0.5800 (t0) REVERT: D 107 LEU cc_start: 0.3280 (tp) cc_final: 0.2860 (tt) REVERT: E 48 GLU cc_start: 0.6999 (tt0) cc_final: 0.6781 (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: 0.0188 (m-10) outliers start: 31 outliers final: 7 residues processed: 470 average time/residue: 0.5751 time to fit residues: 432.4328 Evaluate side-chains 225 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 4.572 ------------------------------------------------------------------------------- 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 413 optimal weight: 20.0000 chunk 371 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 250 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 285 optimal weight: 6.9990 chunk 444 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 448 ASN 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1005 GLN C 66 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 113 GLN I 202 HIS D 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 39674 Z= 0.386 Angle : 0.677 10.255 54047 Z= 0.347 Chirality : 0.047 0.468 6296 Planarity : 0.005 0.087 6903 Dihedral : 5.978 58.989 6505 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.28 % Allowed : 18.42 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 4894 helix: 0.92 (0.20), residues: 705 sheet: 0.05 (0.14), residues: 1417 loop : -1.65 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.010 0.002 HIS C1064 PHE 0.025 0.002 PHE H 177 TYR 0.033 0.002 TYR K 151 ARG 0.008 0.001 ARG B 765 *********************** 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 364 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 224 time to evaluate : 4.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7341 (tmm) cc_final: 0.6075 (pmm) REVERT: A 191 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7669 (mm-30) REVERT: A 331 ASN cc_start: 0.3808 (OUTLIER) cc_final: 0.3308 (p0) REVERT: A 461 LEU cc_start: -0.1289 (OUTLIER) cc_final: -0.3963 (mt) REVERT: A 740 MET cc_start: 0.8281 (mmm) cc_final: 0.8048 (tpt) REVERT: B 106 PHE cc_start: 0.8334 (m-80) cc_final: 0.7857 (m-80) REVERT: B 153 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.5727 (pmm) REVERT: B 202 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8906 (mmtm) REVERT: B 270 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 388 ASN cc_start: 0.1011 (OUTLIER) cc_final: 0.0300 (m-40) REVERT: B 391 CYS cc_start: 0.1904 (OUTLIER) cc_final: 0.1615 (m) REVERT: B 867 ASP cc_start: 0.8538 (m-30) cc_final: 0.8310 (p0) REVERT: B 902 MET cc_start: 0.9200 (tpp) cc_final: 0.8648 (tpp) REVERT: B 957 GLN cc_start: 0.8842 (pt0) cc_final: 0.8231 (pp30) REVERT: B 969 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8175 (m-40) REVERT: B 997 ILE cc_start: 0.9643 (mm) cc_final: 0.9379 (mm) REVERT: B 1086 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7512 (pttm) REVERT: C 201 PHE cc_start: 0.7874 (t80) cc_final: 0.7380 (t80) REVERT: C 342 PHE cc_start: 0.5053 (m-10) cc_final: 0.4153 (t80) REVERT: C 562 PHE cc_start: 0.7719 (p90) cc_final: 0.7362 (p90) REVERT: C 565 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7324 (m-10) REVERT: C 786 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7631 (ptpp) REVERT: C 900 MET cc_start: 0.9203 (mtp) cc_final: 0.8752 (mtm) REVERT: C 947 LYS cc_start: 0.9213 (mppt) cc_final: 0.8974 (mmtp) REVERT: C 1008 VAL cc_start: 0.9614 (t) cc_final: 0.9212 (p) REVERT: G 46 GLU cc_start: 0.6470 (pt0) cc_final: 0.6151 (mm-30) REVERT: I 181 SER cc_start: 0.2226 (m) cc_final: 0.1550 (t) REVERT: E 34 TYR cc_start: 0.5739 (t80) cc_final: 0.4958 (t80) REVERT: E 147 CYS cc_start: 0.1520 (OUTLIER) cc_final: 0.1280 (p) REVERT: K 121 LYS cc_start: 0.4875 (OUTLIER) cc_final: 0.4072 (mppt) outliers start: 140 outliers final: 52 residues processed: 345 average time/residue: 0.5331 time to fit residues: 313.4635 Evaluate side-chains 232 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU 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 331 ASN 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 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 270 LEU 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 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 189 LEU 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 915 VAL Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 118 THR 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 147 CYS Chi-restraints excluded: chain K residue 8 HIS 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 247 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 370 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 445 optimal weight: 5.9990 chunk 481 optimal weight: 0.0670 chunk 397 optimal weight: 30.0000 chunk 442 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 357 optimal weight: 20.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- 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** B 498 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 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 119 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39674 Z= 0.316 Angle : 0.591 9.360 54047 Z= 0.305 Chirality : 0.046 0.491 6296 Planarity : 0.004 0.088 6903 Dihedral : 5.494 57.484 6492 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.78 % Favored : 96.20 % Rotamer: Outliers : 3.07 % Allowed : 18.93 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4894 helix: 1.20 (0.20), residues: 707 sheet: 0.11 (0.14), residues: 1379 loop : -1.53 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 36 HIS 0.007 0.001 HIS C1064 PHE 0.028 0.002 PHE A 133 TYR 0.018 0.001 TYR A 508 ARG 0.006 0.001 ARG B 905 *********************** 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 315 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 184 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7044 (tmm) cc_final: 0.5682 (pmm) REVERT: A 165 ASN cc_start: 0.6480 (OUTLIER) cc_final: 0.6178 (p0) REVERT: A 238 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.7741 (p90) REVERT: A 461 LEU cc_start: -0.2445 (OUTLIER) cc_final: -0.5038 (mt) REVERT: A 873 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: A 1107 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8216 (ptp90) REVERT: B 106 PHE cc_start: 0.8247 (m-80) cc_final: 0.8046 (m-80) REVERT: B 117 LEU cc_start: 0.9175 (tp) cc_final: 0.8903 (mm) REVERT: B 153 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.5766 (pmm) REVERT: B 200 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8607 (t80) REVERT: B 202 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8935 (mmtp) REVERT: B 703 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7777 (p0) REVERT: B 725 GLU cc_start: 0.8576 (tt0) cc_final: 0.8058 (tp30) REVERT: B 867 ASP cc_start: 0.8615 (m-30) cc_final: 0.8342 (p0) REVERT: B 902 MET cc_start: 0.9066 (tpp) cc_final: 0.8768 (tpp) REVERT: B 957 GLN cc_start: 0.8749 (pt0) cc_final: 0.8367 (pp30) REVERT: B 997 ILE cc_start: 0.9649 (mm) cc_final: 0.9383 (mm) REVERT: C 201 PHE cc_start: 0.8147 (t80) cc_final: 0.7775 (t80) REVERT: C 565 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: C 786 LYS cc_start: 0.8529 (mmmt) cc_final: 0.7750 (ptpt) REVERT: C 900 MET cc_start: 0.9207 (mtp) cc_final: 0.8715 (mtp) REVERT: C 947 LYS cc_start: 0.9194 (mppt) cc_final: 0.8970 (mmtm) REVERT: C 955 ASN cc_start: 0.8268 (m-40) cc_final: 0.7526 (t0) REVERT: C 1008 VAL cc_start: 0.9608 (t) cc_final: 0.9297 (p) REVERT: G 46 GLU cc_start: 0.5796 (pt0) cc_final: 0.5551 (mm-30) REVERT: I 181 SER cc_start: 0.2287 (m) cc_final: 0.1919 (t) REVERT: E 34 TYR cc_start: 0.6117 (t80) cc_final: 0.5709 (t80) REVERT: E 147 CYS cc_start: 0.1153 (OUTLIER) cc_final: 0.0520 (m) REVERT: K 121 LYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4173 (mppt) REVERT: M 106 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.6915 (ptp90) REVERT: M 207 HIS cc_start: 0.1461 (t-170) cc_final: 0.1247 (t-170) outliers start: 131 outliers final: 71 residues processed: 301 average time/residue: 0.5077 time to fit residues: 260.3585 Evaluate side-chains 240 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 158 time to evaluate : 4.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 231 ILE 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 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 A residue 1107 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 200 TYR 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 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 859 THR 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 120 VAL 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 231 ILE Chi-restraints excluded: chain C residue 301 CYS 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 539 VAL Chi-restraints excluded: chain C residue 565 PHE 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 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 118 THR 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 E residue 54 TYR 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 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 440 optimal weight: 3.9990 chunk 335 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 447 optimal weight: 0.0670 chunk 473 optimal weight: 0.5980 chunk 233 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 overall best weight: 0.9258 ------------------------------------------------------------------------------- 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 448 ASN A 955 ASN A1083 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN I 53 ASN E 3 GLN M 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 39674 Z= 0.165 Angle : 0.513 12.063 54047 Z= 0.261 Chirality : 0.044 0.472 6296 Planarity : 0.004 0.074 6903 Dihedral : 5.068 59.463 6492 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer: Outliers : 2.44 % Allowed : 19.70 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4894 helix: 1.50 (0.21), residues: 704 sheet: 0.19 (0.14), residues: 1394 loop : -1.45 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 37 HIS 0.004 0.001 HIS A1048 PHE 0.025 0.001 PHE B 186 TYR 0.016 0.001 TYR A 508 ARG 0.004 0.000 ARG H 67 *********************** 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 290 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 186 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.6843 (tmm) cc_final: 0.5639 (pmm) REVERT: A 191 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7388 (mm-30) REVERT: A 461 LEU cc_start: -0.2516 (OUTLIER) cc_final: -0.5030 (mt) REVERT: B 153 MET cc_start: 0.7279 (tmm) cc_final: 0.5743 (pmm) REVERT: B 200 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8505 (t80) REVERT: B 202 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8905 (mmtp) REVERT: B 347 PHE cc_start: -0.0264 (OUTLIER) cc_final: -0.1827 (t80) REVERT: B 725 GLU cc_start: 0.8488 (tt0) cc_final: 0.8030 (tp30) REVERT: B 740 MET cc_start: 0.7250 (ttt) cc_final: 0.6261 (tmm) REVERT: B 780 GLU cc_start: 0.9049 (tt0) cc_final: 0.8841 (tt0) REVERT: B 867 ASP cc_start: 0.8546 (m-30) cc_final: 0.8244 (p0) REVERT: B 869 MET cc_start: 0.9140 (mmm) cc_final: 0.8771 (tpp) REVERT: B 957 GLN cc_start: 0.8658 (pt0) cc_final: 0.8350 (pp30) REVERT: B 997 ILE cc_start: 0.9634 (mm) cc_final: 0.9371 (mm) REVERT: B 1086 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7497 (pttm) REVERT: C 104 TRP cc_start: 0.5530 (m-90) cc_final: 0.5293 (m-90) REVERT: C 518 LEU cc_start: 0.3189 (OUTLIER) cc_final: 0.2149 (mt) REVERT: C 565 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.7502 (m-10) REVERT: C 703 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7773 (p0) REVERT: C 786 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7618 (ptpt) REVERT: C 900 MET cc_start: 0.9145 (mtp) cc_final: 0.8793 (mtm) REVERT: C 902 MET cc_start: 0.9271 (tpp) cc_final: 0.9070 (tpp) REVERT: C 955 ASN cc_start: 0.7979 (m-40) cc_final: 0.7776 (t0) REVERT: C 1008 VAL cc_start: 0.9533 (t) cc_final: 0.9180 (p) REVERT: L 189 GLN cc_start: 0.0174 (OUTLIER) cc_final: -0.0332 (mm-40) REVERT: I 181 SER cc_start: 0.2068 (m) cc_final: 0.1662 (t) REVERT: E 34 TYR cc_start: 0.5750 (t80) cc_final: 0.5400 (t80) REVERT: E 112 GLN cc_start: 0.3487 (pm20) cc_final: 0.2746 (mm110) REVERT: E 147 CYS cc_start: 0.1105 (p) cc_final: 0.0477 (m) REVERT: K 121 LYS cc_start: 0.4634 (OUTLIER) cc_final: 0.4045 (mppt) outliers start: 104 outliers final: 56 residues processed: 282 average time/residue: 0.5222 time to fit residues: 247.2012 Evaluate side-chains 231 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU 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 464 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 662 CYS 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 B residue 42 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain C residue 51 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 231 ILE Chi-restraints excluded: chain C residue 301 CYS 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 518 LEU Chi-restraints excluded: chain C residue 565 PHE 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 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 118 THR 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 189 GLN Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain K residue 8 HIS Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain M residue 21 THR 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 394 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 404 optimal weight: 0.0270 chunk 327 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 425 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 87 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 99 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN 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 113 GLN L 189 GLN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 54 GLN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 39674 Z= 0.603 Angle : 0.816 12.702 54047 Z= 0.416 Chirality : 0.051 0.412 6296 Planarity : 0.005 0.085 6903 Dihedral : 6.149 58.927 6488 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.09 % Favored : 93.89 % Rotamer: Outliers : 4.29 % Allowed : 19.52 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 4894 helix: 0.65 (0.20), residues: 683 sheet: -0.28 (0.13), residues: 1453 loop : -1.64 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 190 HIS 0.016 0.002 HIS C1064 PHE 0.026 0.003 PHE B 329 TYR 0.030 0.002 TYR B 904 ARG 0.016 0.001 ARG H 87 *********************** 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 355 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 172 time to evaluate : 4.829 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: 0.4955 (tmm) cc_final: 0.3861 (pmm) REVERT: A 238 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.7887 (p90) REVERT: A 461 LEU cc_start: -0.1023 (OUTLIER) cc_final: -0.3865 (mt) REVERT: A 900 MET cc_start: 0.9397 (mtt) cc_final: 0.9080 (mtp) REVERT: A 962 LEU cc_start: 0.9590 (tp) cc_final: 0.9347 (tp) REVERT: B 106 PHE cc_start: 0.8572 (m-80) cc_final: 0.8121 (m-80) REVERT: B 153 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.5302 (pmm) REVERT: B 200 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7866 (t80) REVERT: B 202 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8710 (mmtm) REVERT: B 347 PHE cc_start: 0.0141 (OUTLIER) cc_final: -0.1827 (t80) REVERT: B 725 GLU cc_start: 0.8736 (tt0) cc_final: 0.8264 (tp30) REVERT: B 867 ASP cc_start: 0.8696 (m-30) cc_final: 0.8447 (p0) REVERT: B 869 MET cc_start: 0.9374 (mmm) cc_final: 0.9153 (tpp) REVERT: B 895 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.8923 (pm20) REVERT: B 902 MET cc_start: 0.9345 (tpt) cc_final: 0.8851 (tpp) REVERT: B 947 LYS cc_start: 0.9500 (mppt) cc_final: 0.9261 (mtpt) REVERT: B 957 GLN cc_start: 0.9059 (pt0) cc_final: 0.8587 (pp30) REVERT: B 969 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8729 (m-40) REVERT: B 1005 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8915 (tp-100) REVERT: B 1130 ILE cc_start: 0.9032 (pt) cc_final: 0.8712 (mm) REVERT: C 128 ILE cc_start: 0.8754 (mp) cc_final: 0.8486 (pt) REVERT: C 327 VAL cc_start: 0.8781 (t) cc_final: 0.8561 (t) REVERT: C 518 LEU cc_start: 0.3325 (OUTLIER) cc_final: 0.2226 (mt) REVERT: C 786 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7822 (ptpp) REVERT: C 856 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8351 (t0) REVERT: C 900 MET cc_start: 0.9233 (mtp) cc_final: 0.8771 (mtm) REVERT: C 955 ASN cc_start: 0.8246 (m-40) cc_final: 0.7978 (t0) REVERT: L 189 GLN cc_start: 0.1935 (OUTLIER) cc_final: 0.1668 (mp10) REVERT: G 43 GLN cc_start: 0.2060 (OUTLIER) cc_final: 0.1805 (mt0) REVERT: I 181 SER cc_start: 0.2296 (m) cc_final: 0.1970 (t) REVERT: E 75 THR cc_start: 0.5102 (OUTLIER) cc_final: 0.4658 (p) REVERT: E 112 GLN cc_start: 0.4122 (pm20) cc_final: 0.2589 (mm110) REVERT: E 115 LEU cc_start: 0.6034 (OUTLIER) cc_final: 0.5394 (mp) REVERT: E 147 CYS cc_start: 0.2239 (p) cc_final: 0.1843 (m) REVERT: K 121 LYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4257 (mmtt) outliers start: 183 outliers final: 110 residues processed: 336 average time/residue: 0.4906 time to fit residues: 284.3807 Evaluate side-chains 268 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 144 time to evaluate : 4.615 ------------------------------------------------------------------------------- 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 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 734 THR 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 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 19 THR 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 119 ILE 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 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 662 CYS 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 895 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 963 VAL 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 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 135 PHE Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 301 CYS 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 662 CYS 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 856 ASN 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 962 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 1118 ASP Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 118 THR 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 L residue 77 ILE Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain G residue 43 GLN 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 50 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain E residue 52 CYS Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 115 LEU 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 108 THR Chi-restraints excluded: chain K residue 121 LYS Chi-restraints excluded: chain K residue 147 ILE Chi-restraints excluded: chain K residue 186 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 0.9990 chunk 426 optimal weight: 30.0000 chunk 93 optimal weight: 0.6980 chunk 278 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 474 optimal weight: 8.9990 chunk 393 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 544 ASN B 703 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B 992 GLN C 460 ASN C 856 ASN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39674 Z= 0.166 Angle : 0.545 12.165 54047 Z= 0.276 Chirality : 0.045 0.424 6296 Planarity : 0.004 0.081 6903 Dihedral : 5.351 59.301 6488 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 2.53 % Allowed : 20.85 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 4894 helix: 1.29 (0.20), residues: 695 sheet: -0.04 (0.13), residues: 1420 loop : -1.49 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS A1048 PHE 0.026 0.001 PHE A 329 TYR 0.022 0.001 TYR K 151 ARG 0.006 0.000 ARG H 67 *********************** 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 279 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 171 time to evaluate : 4.572 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 153 MET cc_start: 0.5572 (tmm) cc_final: 0.4608 (pmm) REVERT: A 238 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7873 (p90) REVERT: A 461 LEU cc_start: -0.1405 (OUTLIER) cc_final: -0.4132 (mt) REVERT: A 565 PHE cc_start: 0.8718 (m-10) cc_final: 0.8475 (m-80) REVERT: A 740 MET cc_start: 0.7668 (ttt) cc_final: 0.7130 (tmm) REVERT: A 962 LEU cc_start: 0.9530 (tp) cc_final: 0.9292 (tp) REVERT: B 88 ASP cc_start: 0.6955 (p0) cc_final: 0.6383 (p0) REVERT: B 106 PHE cc_start: 0.8295 (m-80) cc_final: 0.7808 (m-80) REVERT: B 153 MET cc_start: 0.7033 (tmm) cc_final: 0.5550 (pmm) REVERT: B 200 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 202 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8798 (mmtp) REVERT: B 347 PHE cc_start: -0.0299 (OUTLIER) cc_final: -0.1864 (t80) REVERT: B 725 GLU cc_start: 0.8608 (tt0) cc_final: 0.8092 (tp30) REVERT: B 867 ASP cc_start: 0.8575 (m-30) cc_final: 0.8359 (p0) REVERT: B 869 MET cc_start: 0.9146 (mmm) cc_final: 0.8877 (tpp) REVERT: B 895 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8249 (pm20) REVERT: B 902 MET cc_start: 0.9339 (tpt) cc_final: 0.9094 (tpt) REVERT: B 947 LYS cc_start: 0.9360 (mppt) cc_final: 0.9047 (mtpt) REVERT: B 957 GLN cc_start: 0.8735 (pt0) cc_final: 0.8382 (pp30) REVERT: B 997 ILE cc_start: 0.9672 (mm) cc_final: 0.9349 (mm) REVERT: B 1005 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8785 (tp40) REVERT: B 1107 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8068 (mtt90) REVERT: C 128 ILE cc_start: 0.8650 (mp) cc_final: 0.8415 (pt) REVERT: C 299 THR cc_start: 0.9228 (m) cc_final: 0.8859 (p) REVERT: C 376 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 518 LEU cc_start: 0.3202 (OUTLIER) cc_final: 0.2133 (mt) REVERT: C 562 PHE cc_start: 0.8145 (p90) cc_final: 0.7751 (p90) REVERT: C 670 ILE cc_start: 0.9189 (tt) cc_final: 0.8862 (mt) REVERT: C 697 MET cc_start: 0.8569 (ttm) cc_final: 0.8264 (ttt) REVERT: C 786 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7760 (ptpt) REVERT: C 856 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8396 (t0) REVERT: C 866 THR cc_start: 0.9152 (p) cc_final: 0.8906 (p) REVERT: C 900 MET cc_start: 0.9043 (mtp) cc_final: 0.8685 (mtm) REVERT: C 1106 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8703 (pt0) REVERT: I 181 SER cc_start: 0.2490 (m) cc_final: 0.2184 (t) REVERT: E 34 TYR cc_start: 0.6253 (t80) cc_final: 0.5834 (t80) REVERT: E 99 ARG cc_start: 0.6020 (ttt90) cc_final: 0.5515 (mtt90) REVERT: E 112 GLN cc_start: 0.3921 (pm20) cc_final: 0.2324 (mm110) REVERT: E 147 CYS cc_start: 0.1132 (OUTLIER) cc_final: 0.0830 (p) REVERT: M 106 ARG cc_start: 0.7669 (ptt-90) cc_final: 0.7138 (ptp90) outliers start: 108 outliers final: 67 residues processed: 270 average time/residue: 0.4980 time to fit residues: 230.6208 Evaluate side-chains 230 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 152 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 866 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 200 TYR 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 662 CYS Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN 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 1123 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 301 CYS 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 539 VAL 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 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 856 ASN 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 C residue 974 SER 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 118 THR 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 L residue 91 GLN Chi-restraints excluded: chain G residue 71 THR 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 101 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 147 CYS 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 118 VAL Chi-restraints excluded: chain M residue 122 SER 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 457 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 270 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 399 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 472 optimal weight: 20.0000 chunk 295 optimal weight: 0.5980 chunk 287 optimal weight: 0.2980 chunk 218 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39674 Z= 0.219 Angle : 0.547 13.815 54047 Z= 0.275 Chirality : 0.045 0.407 6296 Planarity : 0.004 0.077 6903 Dihedral : 5.075 57.397 6484 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % Rotamer: Outliers : 2.44 % Allowed : 21.27 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4894 helix: 1.36 (0.20), residues: 707 sheet: -0.09 (0.13), residues: 1432 loop : -1.38 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 110 HIS 0.004 0.001 HIS A1048 PHE 0.032 0.001 PHE A 329 TYR 0.033 0.001 TYR B 145 ARG 0.009 0.000 ARG H 67 *********************** 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 266 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 162 time to evaluate : 4.276 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: A 153 MET cc_start: 0.5578 (tmm) cc_final: 0.4625 (pmm) REVERT: A 238 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 461 LEU cc_start: -0.1329 (OUTLIER) cc_final: -0.4059 (mt) REVERT: A 565 PHE cc_start: 0.8802 (m-10) cc_final: 0.8549 (m-80) REVERT: A 740 MET cc_start: 0.7653 (ttt) cc_final: 0.7108 (tmm) REVERT: A 774 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8488 (mm-40) REVERT: B 106 PHE cc_start: 0.8413 (m-80) cc_final: 0.7953 (m-80) REVERT: B 153 MET cc_start: 0.7034 (tmm) cc_final: 0.5562 (pmm) REVERT: B 200 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8035 (t80) REVERT: B 202 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8789 (mmtp) REVERT: B 347 PHE cc_start: -0.1155 (OUTLIER) cc_final: -0.3025 (t80) REVERT: B 670 ILE cc_start: 0.8835 (tt) cc_final: 0.8634 (mt) REVERT: B 724 THR cc_start: 0.9664 (OUTLIER) cc_final: 0.9438 (t) REVERT: B 725 GLU cc_start: 0.8668 (tt0) cc_final: 0.8120 (tp30) REVERT: B 740 MET cc_start: 0.7811 (tmm) cc_final: 0.7187 (tmm) REVERT: B 867 ASP cc_start: 0.8606 (m-30) cc_final: 0.8389 (p0) REVERT: B 869 MET cc_start: 0.9151 (mmm) cc_final: 0.8891 (tpp) REVERT: B 902 MET cc_start: 0.9376 (tpt) cc_final: 0.9163 (tpt) REVERT: B 947 LYS cc_start: 0.9442 (mppt) cc_final: 0.9093 (mtpt) REVERT: B 957 GLN cc_start: 0.8801 (pt0) cc_final: 0.8346 (pp30) REVERT: B 997 ILE cc_start: 0.9655 (mm) cc_final: 0.9366 (mm) REVERT: B 1107 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8085 (mtt90) REVERT: C 128 ILE cc_start: 0.8638 (mp) cc_final: 0.8404 (pt) REVERT: C 299 THR cc_start: 0.9237 (m) cc_final: 0.8883 (p) REVERT: C 518 LEU cc_start: 0.3213 (OUTLIER) cc_final: 0.2136 (mt) REVERT: C 670 ILE cc_start: 0.9231 (tt) cc_final: 0.8848 (mm) REVERT: C 697 MET cc_start: 0.8731 (ttm) cc_final: 0.8441 (ttt) REVERT: C 786 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7682 (ptpt) REVERT: C 866 THR cc_start: 0.9183 (p) cc_final: 0.8951 (p) REVERT: C 900 MET cc_start: 0.9112 (mtp) cc_final: 0.8730 (mtm) REVERT: C 902 MET cc_start: 0.9373 (tpp) cc_final: 0.9156 (tpp) REVERT: C 1106 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8648 (pt0) REVERT: H 87 ARG cc_start: 0.4929 (mtt90) cc_final: 0.4172 (mpp80) REVERT: I 181 SER cc_start: 0.2440 (m) cc_final: 0.2128 (t) REVERT: E 34 TYR cc_start: 0.6243 (t80) cc_final: 0.5980 (t80) REVERT: E 99 ARG cc_start: 0.6147 (ttt90) cc_final: 0.5688 (mtt90) REVERT: E 112 GLN cc_start: 0.4048 (pm20) cc_final: 0.2538 (mm110) REVERT: E 147 CYS cc_start: 0.1604 (OUTLIER) cc_final: 0.1109 (m) outliers start: 104 outliers final: 81 residues processed: 258 average time/residue: 0.4951 time to fit residues: 221.5020 Evaluate side-chains 243 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 153 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 721 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU 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 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR 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 483 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 724 THR 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 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 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 227 VAL 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 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 703 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER 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 974 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 118 THR 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 L residue 101 VAL 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 50 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain D residue 12 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 147 CYS 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 118 VAL Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 282 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 321 optimal weight: 50.0000 chunk 233 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 371 optimal weight: 40.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 GLN B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN D 54 GLN E 3 GLN M 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39674 Z= 0.203 Angle : 0.536 17.417 54047 Z= 0.268 Chirality : 0.044 0.390 6296 Planarity : 0.004 0.077 6903 Dihedral : 4.851 57.859 6484 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 2.58 % Allowed : 21.32 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 4894 helix: 1.51 (0.21), residues: 691 sheet: -0.07 (0.14), residues: 1428 loop : -1.30 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP I 37 HIS 0.004 0.001 HIS C1064 PHE 0.029 0.001 PHE A 329 TYR 0.020 0.001 TYR A 380 ARG 0.005 0.000 ARG H 67 *********************** 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 274 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 164 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7922 (p90) REVERT: A 461 LEU cc_start: -0.1132 (OUTLIER) cc_final: -0.3983 (mt) REVERT: A 740 MET cc_start: 0.7628 (ttt) cc_final: 0.7134 (tmm) REVERT: A 774 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8352 (mm-40) REVERT: A 962 LEU cc_start: 0.9501 (tp) cc_final: 0.9259 (tp) REVERT: B 106 PHE cc_start: 0.8343 (m-80) cc_final: 0.7883 (m-80) REVERT: B 153 MET cc_start: 0.6720 (tmm) cc_final: 0.5252 (pmm) REVERT: B 200 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7946 (t80) REVERT: B 202 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8824 (mmtp) REVERT: B 347 PHE cc_start: -0.0475 (OUTLIER) cc_final: -0.2142 (t80) REVERT: B 670 ILE cc_start: 0.8833 (tt) cc_final: 0.8615 (mt) REVERT: B 724 THR cc_start: 0.9646 (OUTLIER) cc_final: 0.9436 (t) REVERT: B 725 GLU cc_start: 0.8649 (tt0) cc_final: 0.8113 (tp30) REVERT: B 740 MET cc_start: 0.7835 (tmm) cc_final: 0.7494 (tmm) REVERT: B 867 ASP cc_start: 0.8593 (m-30) cc_final: 0.8384 (p0) REVERT: B 869 MET cc_start: 0.9127 (mmm) cc_final: 0.8838 (tpp) REVERT: B 902 MET cc_start: 0.9374 (tpt) cc_final: 0.9140 (tpt) REVERT: B 947 LYS cc_start: 0.9402 (mppt) cc_final: 0.9119 (mtpt) REVERT: B 957 GLN cc_start: 0.8776 (pt0) cc_final: 0.8342 (pp30) REVERT: B 997 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9368 (mm) REVERT: B 1086 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7842 (pttp) REVERT: B 1107 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8141 (mtt90) REVERT: C 128 ILE cc_start: 0.8569 (mp) cc_final: 0.8352 (pt) REVERT: C 299 THR cc_start: 0.9233 (m) cc_final: 0.8895 (p) REVERT: C 518 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.2245 (mt) REVERT: C 670 ILE cc_start: 0.9210 (tt) cc_final: 0.8841 (mm) REVERT: C 697 MET cc_start: 0.8701 (ttm) cc_final: 0.8355 (ttt) REVERT: C 786 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7825 (ptpt) REVERT: C 900 MET cc_start: 0.9103 (mtp) cc_final: 0.8705 (mtm) REVERT: C 1106 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8598 (pt0) REVERT: H 87 ARG cc_start: 0.5182 (mtt90) cc_final: 0.4957 (mtt90) REVERT: L 189 GLN cc_start: 0.0345 (OUTLIER) cc_final: -0.0159 (mm-40) REVERT: I 181 SER cc_start: 0.2431 (m) cc_final: 0.2091 (t) REVERT: E 34 TYR cc_start: 0.6088 (t80) cc_final: 0.5701 (t80) REVERT: E 147 CYS cc_start: 0.1603 (OUTLIER) cc_final: 0.1113 (m) REVERT: M 207 HIS cc_start: 0.0673 (t-170) cc_final: -0.0352 (t-90) outliers start: 110 outliers final: 83 residues processed: 265 average time/residue: 0.4876 time to fit residues: 225.2901 Evaluate side-chains 253 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 158 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 662 CYS 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 937 SER Chi-restraints excluded: chain A residue 959 LEU 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 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR 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 483 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 724 THR 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 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 997 ILE 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 374 PHE 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 538 CYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 549 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 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 878 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 1037 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain G residue 71 THR 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 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 12 GLU Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 147 CYS 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 118 VAL Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 40.0000 chunk 452 optimal weight: 0.8980 chunk 412 optimal weight: 10.0000 chunk 440 optimal weight: 2.9990 chunk 264 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 345 optimal weight: 30.0000 chunk 135 optimal weight: 2.9990 chunk 397 optimal weight: 20.0000 chunk 416 optimal weight: 20.0000 chunk 438 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** B 774 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 GLN D 54 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 39674 Z= 0.262 Angle : 0.563 17.981 54047 Z= 0.281 Chirality : 0.045 0.382 6296 Planarity : 0.004 0.078 6903 Dihedral : 4.903 58.096 6484 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.66 % Favored : 95.30 % Rotamer: Outliers : 2.72 % Allowed : 21.34 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 4894 helix: 1.55 (0.21), residues: 679 sheet: -0.08 (0.14), residues: 1421 loop : -1.29 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.005 0.001 HIS A1048 PHE 0.030 0.001 PHE A 329 TYR 0.018 0.001 TYR A 365 ARG 0.008 0.000 ARG D 55 *********************** 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 271 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 155 time to evaluate : 4.476 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: A 153 MET cc_start: 0.6616 (ppp) cc_final: 0.5602 (pmm) REVERT: A 238 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7943 (p90) REVERT: A 461 LEU cc_start: -0.1779 (OUTLIER) cc_final: -0.4519 (mt) REVERT: A 774 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8332 (mm-40) REVERT: A 962 LEU cc_start: 0.9514 (tp) cc_final: 0.9284 (tp) REVERT: B 106 PHE cc_start: 0.8484 (m-80) cc_final: 0.7945 (m-80) REVERT: B 153 MET cc_start: 0.6731 (tmm) cc_final: 0.5245 (pmm) REVERT: B 200 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8095 (t80) REVERT: B 202 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8828 (mmtp) REVERT: B 347 PHE cc_start: 0.0867 (OUTLIER) cc_final: -0.1579 (t80) REVERT: B 725 GLU cc_start: 0.8726 (tt0) cc_final: 0.8208 (tp30) REVERT: B 740 MET cc_start: 0.7955 (tmm) cc_final: 0.7580 (tmm) REVERT: B 867 ASP cc_start: 0.8613 (m-30) cc_final: 0.8400 (p0) REVERT: B 895 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: B 902 MET cc_start: 0.9377 (tpt) cc_final: 0.8752 (tpp) REVERT: B 947 LYS cc_start: 0.9428 (mppt) cc_final: 0.9140 (mtpt) REVERT: B 957 GLN cc_start: 0.8815 (pt0) cc_final: 0.8373 (pp30) REVERT: B 969 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8603 (m-40) REVERT: B 997 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9353 (mm) REVERT: B 1086 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7848 (pttp) REVERT: B 1107 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8062 (mtt90) REVERT: C 128 ILE cc_start: 0.8599 (mp) cc_final: 0.8384 (pt) REVERT: C 299 THR cc_start: 0.9261 (m) cc_final: 0.8927 (p) REVERT: C 518 LEU cc_start: 0.3420 (OUTLIER) cc_final: 0.2246 (mt) REVERT: C 670 ILE cc_start: 0.9121 (tt) cc_final: 0.8718 (mt) REVERT: C 786 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7701 (ptpt) REVERT: C 900 MET cc_start: 0.9138 (mtp) cc_final: 0.8806 (mtp) REVERT: C 1106 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8810 (pt0) REVERT: H 87 ARG cc_start: 0.5217 (mtt90) cc_final: 0.5008 (mtt90) REVERT: L 189 GLN cc_start: 0.0685 (OUTLIER) cc_final: 0.0346 (mm-40) REVERT: I 181 SER cc_start: 0.2615 (m) cc_final: 0.2250 (t) REVERT: E 34 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5820 (t80) REVERT: E 147 CYS cc_start: 0.1707 (OUTLIER) cc_final: 0.1176 (m) REVERT: M 207 HIS cc_start: 0.0762 (t-170) cc_final: -0.0283 (t-90) outliers start: 116 outliers final: 92 residues processed: 264 average time/residue: 0.5297 time to fit residues: 245.2393 Evaluate side-chains 254 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 148 time to evaluate : 5.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 662 CYS Chi-restraints excluded: chain A residue 721 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 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU 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 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR 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 483 VAL Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1123 SER 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 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 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 703 ASN 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 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL 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 69 THR Chi-restraints excluded: chain H residue 118 THR 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 L residue 101 VAL Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 71 THR 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 12 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 147 CYS 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 118 VAL Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 0.0970 chunk 465 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 323 optimal weight: 1.9990 chunk 488 optimal weight: 6.9990 chunk 449 optimal weight: 8.9990 chunk 388 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 300 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1005 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 39674 Z= 0.237 Angle : 0.550 18.361 54047 Z= 0.275 Chirality : 0.044 0.378 6296 Planarity : 0.004 0.078 6903 Dihedral : 4.856 58.220 6484 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 2.58 % Allowed : 21.60 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4894 helix: 1.51 (0.21), residues: 683 sheet: -0.05 (0.14), residues: 1412 loop : -1.29 (0.12), residues: 2799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 36 HIS 0.005 0.001 HIS A1048 PHE 0.029 0.001 PHE A 329 TYR 0.019 0.001 TYR A 380 ARG 0.005 0.000 ARG C1091 ********************** 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 268 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 158 time to evaluate : 4.554 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: A 153 MET cc_start: 0.6589 (ppp) cc_final: 0.5950 (pmm) REVERT: A 238 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7944 (p90) REVERT: A 461 LEU cc_start: -0.1691 (OUTLIER) cc_final: -0.4399 (mt) REVERT: A 774 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8348 (mm-40) REVERT: A 962 LEU cc_start: 0.9512 (tp) cc_final: 0.9277 (tp) REVERT: B 106 PHE cc_start: 0.8515 (m-80) cc_final: 0.7997 (m-80) REVERT: B 153 MET cc_start: 0.6736 (tmm) cc_final: 0.5255 (pmm) REVERT: B 200 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8058 (t80) REVERT: B 202 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8821 (mmtp) REVERT: B 347 PHE cc_start: 0.1483 (OUTLIER) cc_final: -0.1127 (t80) REVERT: B 725 GLU cc_start: 0.8731 (tt0) cc_final: 0.8194 (tp30) REVERT: B 740 MET cc_start: 0.7944 (tmm) cc_final: 0.7562 (tmm) REVERT: B 867 ASP cc_start: 0.8590 (m-30) cc_final: 0.8376 (p0) REVERT: B 869 MET cc_start: 0.9186 (mmt) cc_final: 0.8971 (mmt) REVERT: B 895 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: B 902 MET cc_start: 0.9380 (tpt) cc_final: 0.9148 (tpt) REVERT: B 947 LYS cc_start: 0.9415 (mppt) cc_final: 0.9132 (mtpt) REVERT: B 957 GLN cc_start: 0.8812 (pt0) cc_final: 0.8407 (pp30) REVERT: B 997 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9363 (mm) REVERT: B 1086 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7865 (pttp) REVERT: B 1107 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8105 (mtt90) REVERT: C 128 ILE cc_start: 0.8587 (mp) cc_final: 0.8374 (pt) REVERT: C 299 THR cc_start: 0.9260 (m) cc_final: 0.8937 (p) REVERT: C 518 LEU cc_start: 0.3392 (OUTLIER) cc_final: 0.2231 (mt) REVERT: C 562 PHE cc_start: 0.8210 (p90) cc_final: 0.7964 (p90) REVERT: C 670 ILE cc_start: 0.9074 (tt) cc_final: 0.8650 (mt) REVERT: C 697 MET cc_start: 0.8675 (ttm) cc_final: 0.8409 (ttt) REVERT: C 786 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7697 (ptpt) REVERT: C 900 MET cc_start: 0.9194 (mtp) cc_final: 0.8810 (mtm) REVERT: C 1106 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8791 (pt0) REVERT: I 181 SER cc_start: 0.2665 (m) cc_final: 0.2270 (t) REVERT: E 34 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5818 (t80) REVERT: E 147 CYS cc_start: 0.1658 (OUTLIER) cc_final: 0.1163 (m) REVERT: M 207 HIS cc_start: 0.0645 (t-170) cc_final: -0.0375 (t-90) outliers start: 110 outliers final: 93 residues processed: 259 average time/residue: 0.4841 time to fit residues: 218.3733 Evaluate side-chains 260 residues out of total 4276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 155 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE 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 662 CYS Chi-restraints excluded: chain A residue 721 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 922 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 LEU 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 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR 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 483 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1123 SER 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 415 THR 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 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 703 ASN 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 896 ILE Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL 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 69 THR Chi-restraints excluded: chain H residue 118 THR 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 L residue 101 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 71 THR 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 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 12 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 34 TYR Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 147 CYS 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 21 THR Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain M residue 148 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 2.9990 chunk 414 optimal weight: 40.0000 chunk 119 optimal weight: 0.4980 chunk 358 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 389 optimal weight: 0.5980 chunk 162 optimal weight: 6.9990 chunk 399 optimal weight: 0.1980 chunk 49 optimal weight: 9.9990 chunk 71 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 901 GLN A 992 GLN B 211 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B1005 GLN ** C 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 189 GLN ** G 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.141998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097309 restraints weight = 143802.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094566 restraints weight = 95425.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.094527 restraints weight = 81401.239| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39674 Z= 0.140 Angle : 0.513 18.782 54047 Z= 0.256 Chirality : 0.044 0.372 6296 Planarity : 0.004 0.076 6903 Dihedral : 4.454 58.258 6484 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 2.11 % Allowed : 22.09 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4894 helix: 1.78 (0.21), residues: 670 sheet: 0.00 (0.14), residues: 1396 loop : -1.19 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.004 0.001 HIS A1048 PHE 0.023 0.001 PHE A 329 TYR 0.022 0.001 TYR A 380 ARG 0.005 0.000 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6976.28 seconds wall clock time: 131 minutes 13.99 seconds (7873.99 seconds total)