Starting phenix.real_space_refine on Wed Jan 15 11:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.map" model { file = "/net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y16_38826/01_2025/8y16_38826.cif" } resolution = 2.98 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= -0.001 sd= 0.019 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 14601 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 193 5.16 5 C 25230 2.51 5 N 6435 2.21 5 O 7649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 39510 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 7851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7851 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 6 Chain: "C" Number of atoms: 7963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7963 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 55, 'TRANS': 959} Chain breaks: 6 Chain: "D" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7970 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 55, 'TRANS': 960} Chain breaks: 6 Chain: "E" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "F" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" 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: "Y" 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 21.84, per 1000 atoms: 0.55 Number of scatterers: 39510 At special positions: 0 Unit cell: (175.26, 179.4, 229.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 193 16.00 O 7649 8.00 N 6435 7.00 C 25230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 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=2.31 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 432 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 354 " " NAG B1308 " - " ASN B1074 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C 717 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C1134 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 282 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 165 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 709 " " NAG D1305 " - " ASN D 717 " " NAG D1306 " - " ASN D1098 " " NAG D1307 " - " ASN D 282 " " NAG D1308 " - " ASN D1074 " " NAG D1309 " - " ASN D 657 " " NAG D1310 " - " ASN D 354 " " NAG D1311 " - " ASN D 331 " " NAG D1312 " - " ASN D1134 " " NAG D1313 " - " ASN D 603 " " NAG D1314 " - " ASN D 122 " " NAG E 702 " - " ASN E 53 " " NAG E 703 " - " ASN E 432 " " NAG F 702 " - " ASN F 53 " " NAG F 703 " - " ASN F 432 " " NAG G 1 " - " ASN A 90 " " NAG H 1 " - " ASN A 322 " " NAG I 1 " - " ASN A 546 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 343 " " NAG P 1 " - " ASN D 801 " " NAG Q 1 " - " ASN D 343 " " NAG R 1 " - " ASN E 90 " " NAG S 1 " - " ASN E 322 " " NAG T 1 " - " ASN E 546 " " NAG U 1 " - " ASN E 103 " " NAG V 1 " - " ASN F 90 " " NAG W 1 " - " ASN F 322 " " NAG X 1 " - " ASN F 546 " " NAG Y 1 " - " ASN F 103 " Time building additional restraints: 8.10 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 378 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 378 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 374 " 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9072 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 56 sheets defined 41.2% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.531A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.536A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 83 removed outlier: 3.836A pdb=" N TYR A 83 " --> pdb=" O ALA A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.917A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.951A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 194 removed outlier: 3.740A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.093A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.581A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.754A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.627A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 4.240A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.796A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.735A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.562A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.766A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 587 removed outlier: 3.530A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 295 through 304 removed outlier: 4.990A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.730A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.819A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.546A pdb=" N ASP B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 616 through 625 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.542A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.659A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.682A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.567A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.702A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.769A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.628A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 295 through 304 removed outlier: 5.071A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.626A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.819A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 442 removed outlier: 3.547A pdb=" N ASP C 442 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 617 through 626 removed outlier: 3.733A pdb=" N SER C 621 " --> pdb=" O CYS C 617 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.653A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.577A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 removed outlier: 3.784A pdb=" N LYS C 814 " --> pdb=" O LYS C 811 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG C 815 " --> pdb=" O PRO C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 815' Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.597A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.872A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.700A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.759A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.652A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.550A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 295 through 304 removed outlier: 5.017A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.761A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.819A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 439 through 442 removed outlier: 3.546A pdb=" N ASP D 442 " --> pdb=" O ASN D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 616 through 627 Processing helix chain 'D' and resid 638 through 640 No H-bonds generated for 'chain 'D' and resid 638 through 640' Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.538A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.715A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.620A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 815 removed outlier: 3.613A pdb=" N LYS D 814 " --> pdb=" O LYS D 811 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG D 815 " --> pdb=" O PRO D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 811 through 815' Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 890 removed outlier: 3.819A pdb=" N GLY D 889 " --> pdb=" O TRP D 886 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA D 890 " --> pdb=" O THR D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 890' Processing helix chain 'D' and resid 897 through 910 Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.666A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.691A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.613A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 removed outlier: 3.661A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.502A pdb=" N GLU D1017 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.068A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 79 removed outlier: 3.536A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU E 79 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 removed outlier: 3.836A pdb=" N TYR E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.918A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.952A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 144 through 154 removed outlier: 3.621A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 194 removed outlier: 3.740A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 248 removed outlier: 4.093A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.581A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.754A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.627A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 433 through 447 removed outlier: 4.240A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.796A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.735A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.562A pdb=" N LYS E 541 " --> pdb=" O PRO E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.767A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.531A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 4.068A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.536A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 83 removed outlier: 3.835A pdb=" N TYR F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 80 through 83' Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.918A pdb=" N GLU F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 88 " --> pdb=" O LEU F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 88' Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.952A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 194 removed outlier: 3.741A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 248 removed outlier: 4.093A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 317 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.581A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.754A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.628A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 413 " --> pdb=" O SER F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 433 through 447 removed outlier: 4.240A pdb=" N ASN F 437 " --> pdb=" O GLU F 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.797A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 3.736A pdb=" N THR F 517 " --> pdb=" O ILE F 513 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.562A pdb=" N LYS F 541 " --> pdb=" O PRO F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.767A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 Processing helix chain 'F' and resid 581 through 587 removed outlier: 3.531A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.468A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.110A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.562A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.160A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.520A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 120 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.045A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.506A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.024A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 435 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.204A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.960A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 667 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB7, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.346A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B1065 " --> pdb=" O MET B1050 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.861A pdb=" N ILE B 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 'B' and resid 1120 through 1125 removed outlier: 3.525A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC3, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.599A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.610A pdb=" N PHE C 43 " --> pdb=" O PHE D 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.249A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.561A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AC8, first strand: chain 'C' and resid 317 through 319 removed outlier: 3.641A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.255A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.780A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.023A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 435 " --> pdb=" O ALA C 376 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD4, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.742A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.517A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.551A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.970A pdb=" N ILE C 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 1076 through 1077 removed outlier: 3.601A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.965A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.304A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR D 63 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 48 through 55 removed outlier: 4.267A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.666A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AE5, first strand: chain 'D' and resid 317 through 319 removed outlier: 3.849A pdb=" N GLY D 593 " --> pdb=" O PHE D 318 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 324 through 328 removed outlier: 3.992A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D 553 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.509A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.024A pdb=" N ALA D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 435 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.215A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 667 " --> pdb=" O VAL D 670 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 711 through 728 removed outlier: 7.040A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 711 through 728 removed outlier: 7.040A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.591A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1081 through 1082 removed outlier: 4.583A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF7, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.468A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.110A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 131 through 133 Processing sheet with id=AG1, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.468A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.109A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1616 hydrogen bonds defined for protein. 4539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.13 Time building geometry restraints manager: 9.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11911 1.34 - 1.46: 9898 1.46 - 1.58: 18414 1.58 - 1.71: 3 1.71 - 1.83: 282 Bond restraints: 40508 Sorted by residual: bond pdb=" N GLU F 145 " pdb=" CA GLU F 145 " ideal model delta sigma weight residual 1.462 1.495 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" N ILE C 358 " pdb=" CA ILE C 358 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" N GLU D 324 " pdb=" CA GLU D 324 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.16e-02 7.43e+03 9.98e+00 bond pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.90e+00 bond pdb=" N VAL D 524 " pdb=" CA VAL D 524 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 40503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 53727 2.01 - 4.01: 1210 4.01 - 6.02: 141 6.02 - 8.02: 19 8.02 - 10.03: 9 Bond angle restraints: 55106 Sorted by residual: angle pdb=" N PRO C 527 " pdb=" CA PRO C 527 " pdb=" C PRO C 527 " ideal model delta sigma weight residual 113.40 104.79 8.61 1.34e+00 5.57e-01 4.13e+01 angle pdb=" N PRO D 527 " pdb=" CA PRO D 527 " pdb=" C PRO D 527 " ideal model delta sigma weight residual 113.40 104.79 8.61 1.34e+00 5.57e-01 4.12e+01 angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 113.40 104.81 8.59 1.34e+00 5.57e-01 4.11e+01 angle pdb=" N THR D 356 " pdb=" CA THR D 356 " pdb=" C THR D 356 " ideal model delta sigma weight residual 109.96 100.73 9.23 1.49e+00 4.50e-01 3.84e+01 angle pdb=" C THR D 356 " pdb=" CA THR D 356 " pdb=" CB THR D 356 " ideal model delta sigma weight residual 110.16 118.62 -8.46 1.44e+00 4.82e-01 3.45e+01 ... (remaining 55101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 23254 21.24 - 42.47: 1449 42.47 - 63.71: 214 63.71 - 84.94: 89 84.94 - 106.18: 35 Dihedral angle restraints: 25041 sinusoidal: 10942 harmonic: 14099 Sorted by residual: dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 488 " pdb=" CB CYS D 488 " ideal model delta sinusoidal sigma weight residual -86.00 -167.97 81.97 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -167.95 81.95 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -167.92 81.92 1 1.00e+01 1.00e-02 8.25e+01 ... (remaining 25038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 6250 0.305 - 0.611: 19 0.611 - 0.916: 9 0.916 - 1.221: 0 1.221 - 1.526: 1 Chirality restraints: 6279 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.71e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.69e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.62e+02 ... (remaining 6276 not shown) Planarity restraints: 7058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.317 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG N 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.154 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.486 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 2 " 0.298 2.00e-02 2.50e+03 2.57e-01 8.27e+02 pdb=" C7 NAG O 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG O 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG O 2 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG O 2 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.298 2.00e-02 2.50e+03 2.57e-01 8.26e+02 pdb=" C7 NAG M 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 7055 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 465 2.65 - 3.21: 35624 3.21 - 3.78: 56518 3.78 - 4.34: 76321 4.34 - 4.90: 125838 Nonbonded interactions: 294766 Sorted by model distance: nonbonded pdb=" O ASN B 61 " pdb=" OD1 ASN B 61 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OE2 GLU E 402 " pdb="ZN ZN E 701 " model vdw 2.100 2.230 nonbonded pdb=" OE2 GLU F 402 " pdb="ZN ZN F 701 " model vdw 2.100 2.230 nonbonded pdb=" OE1 GLU F 402 " pdb="ZN ZN F 701 " model vdw 2.107 2.230 ... (remaining 294761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 33 or resid 35 through 614 or resid 701 through \ 703)) selection = (chain 'E' and (resid 19 through 33 or resid 35 through 614 or resid 701 through \ 703)) selection = (chain 'F' and (resid 19 through 33 or resid 35 through 614 or resid 701 through \ 703)) } ncs_group { reference = (chain 'B' and (resid 26 through 826 or resid 855 through 1140 or resid 1301 thr \ ough 1308)) selection = (chain 'C' and (resid 26 through 135 or resid 159 through 1140 or resid 1301 thr \ ough 1308)) selection = (chain 'D' and (resid 26 through 135 or resid 159 through 826 or resid 855 throu \ gh 1140 or resid 1301 through 1308)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.050 Extract box with map and model: 1.440 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 84.220 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4665 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40508 Z= 0.268 Angle : 0.679 10.031 55106 Z= 0.390 Chirality : 0.062 1.526 6279 Planarity : 0.011 0.273 7002 Dihedral : 14.691 106.179 15849 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.86 % Rotamer: Outliers : 0.12 % Allowed : 0.49 % Favored : 99.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.12), residues: 4775 helix: 2.13 (0.13), residues: 1622 sheet: -0.37 (0.23), residues: 510 loop : -1.63 (0.12), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 203 HIS 0.012 0.001 HIS F 401 PHE 0.026 0.001 PHE D 392 TYR 0.012 0.001 TYR F 385 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 327 time to evaluate : 3.286 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 297 MET cc_start: 0.0039 (mmm) cc_final: -0.0887 (mtp) REVERT: A 474 MET cc_start: -0.1061 (mmt) cc_final: -0.1457 (pmm) REVERT: E 123 MET cc_start: 0.0607 (mtm) cc_final: -0.2529 (tpp) REVERT: E 216 ASP cc_start: 0.6123 (m-30) cc_final: 0.5416 (t70) REVERT: F 408 MET cc_start: -0.0657 (mmt) cc_final: -0.1536 (ptp) outliers start: 5 outliers final: 1 residues processed: 332 average time/residue: 1.2503 time to fit residues: 503.9922 Evaluate side-chains 157 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 404 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 201 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 145 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 434 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 487 ASN C 487 ASN C 751 ASN D 487 ASN D 914 ASN D1088 HIS E 149 ASN E 505 HIS ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 81 GLN F 505 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.140375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.098133 restraints weight = 288262.275| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 11.81 r_work: 0.3299 rms_B_bonded: 8.41 restraints_weight: 2.0000 r_work: 0.3367 rms_B_bonded: 6.38 restraints_weight: 4.0000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 40508 Z= 0.197 Angle : 0.630 15.075 55106 Z= 0.318 Chirality : 0.046 0.402 6279 Planarity : 0.004 0.056 7002 Dihedral : 8.738 71.582 6868 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 0.82 % Allowed : 7.23 % Favored : 91.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.12), residues: 4775 helix: 1.95 (0.13), residues: 1662 sheet: 0.11 (0.21), residues: 621 loop : -1.73 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 566 HIS 0.008 0.001 HIS E 505 PHE 0.034 0.001 PHE E 512 TYR 0.020 0.001 TYR D1067 ARG 0.010 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 TRP cc_start: 0.6066 (m100) cc_final: 0.5846 (m100) REVERT: A 564 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7172 (pm20) REVERT: C 565 PHE cc_start: 0.8157 (p90) cc_final: 0.7796 (p90) REVERT: C 740 MET cc_start: 0.9332 (tmm) cc_final: 0.9002 (tmm) REVERT: C 988 GLU cc_start: 0.9362 (mp0) cc_final: 0.9127 (mp0) REVERT: E 123 MET cc_start: 0.1738 (mtm) cc_final: -0.0313 (tpp) REVERT: E 172 VAL cc_start: 0.4938 (t) cc_final: 0.4672 (p) REVERT: E 376 MET cc_start: 0.4591 (tpt) cc_final: 0.3803 (mtt) REVERT: E 474 MET cc_start: 0.3459 (mmt) cc_final: 0.2971 (pp-130) REVERT: E 497 TYR cc_start: -0.0023 (m-80) cc_final: -0.0502 (p90) outliers start: 35 outliers final: 10 residues processed: 201 average time/residue: 1.2509 time to fit residues: 307.9316 Evaluate side-chains 148 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 236 optimal weight: 0.9990 chunk 287 optimal weight: 40.0000 chunk 339 optimal weight: 2.9990 chunk 464 optimal weight: 9.9990 chunk 308 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1083 HIS E 149 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 417 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.138767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.096481 restraints weight = 285908.199| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 11.48 r_work: 0.3246 rms_B_bonded: 8.99 restraints_weight: 2.0000 r_work: 0.3331 rms_B_bonded: 6.28 restraints_weight: 4.0000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 40508 Z= 0.266 Angle : 0.632 15.710 55106 Z= 0.316 Chirality : 0.045 0.413 6279 Planarity : 0.004 0.064 7002 Dihedral : 7.341 59.736 6866 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.49 % Favored : 94.36 % Rotamer: Outliers : 1.20 % Allowed : 9.21 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.12), residues: 4775 helix: 1.65 (0.13), residues: 1699 sheet: -0.21 (0.22), residues: 582 loop : -1.69 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 275 HIS 0.007 0.001 HIS F 540 PHE 0.029 0.002 PHE D 374 TYR 0.019 0.001 TYR D1067 ARG 0.009 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASN cc_start: 0.5888 (m-40) cc_final: 0.5587 (p0) REVERT: A 474 MET cc_start: 0.3583 (OUTLIER) cc_final: -0.0581 (pmm) REVERT: A 564 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7298 (pm20) REVERT: C 740 MET cc_start: 0.9309 (tmm) cc_final: 0.8868 (tmm) REVERT: C 988 GLU cc_start: 0.9368 (mp0) cc_final: 0.9127 (mp0) REVERT: D 133 PHE cc_start: 0.8614 (m-10) cc_final: 0.7707 (m-80) REVERT: D 214 ARG cc_start: 0.2156 (OUTLIER) cc_final: 0.1221 (mmp-170) REVERT: E 123 MET cc_start: 0.1862 (mtm) cc_final: -0.0653 (tpp) REVERT: E 150 GLU cc_start: -0.2142 (OUTLIER) cc_final: -0.2484 (mp0) REVERT: E 474 MET cc_start: 0.2865 (mmt) cc_final: 0.2537 (pp-130) REVERT: E 480 MET cc_start: 0.0903 (OUTLIER) cc_final: 0.0669 (ppp) REVERT: E 497 TYR cc_start: 0.0638 (m-80) cc_final: -0.0077 (p90) REVERT: E 513 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5492 (tp) outliers start: 51 outliers final: 12 residues processed: 176 average time/residue: 1.2675 time to fit residues: 273.0910 Evaluate side-chains 150 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 445 optimal weight: 10.0000 chunk 350 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 320 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 360 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN E 101 GLN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.138665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.096830 restraints weight = 306582.636| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 11.58 r_work: 0.3261 rms_B_bonded: 9.30 restraints_weight: 2.0000 r_work: 0.3298 rms_B_bonded: 6.57 restraints_weight: 4.0000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 40508 Z= 0.224 Angle : 0.599 12.251 55106 Z= 0.300 Chirality : 0.045 0.519 6279 Planarity : 0.004 0.063 7002 Dihedral : 6.480 56.182 6866 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.55 % Favored : 94.30 % Rotamer: Outliers : 1.20 % Allowed : 10.67 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.12), residues: 4775 helix: 1.66 (0.13), residues: 1697 sheet: -0.20 (0.21), residues: 629 loop : -1.62 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 163 HIS 0.009 0.001 HIS F 540 PHE 0.016 0.001 PHE C1089 TYR 0.025 0.001 TYR C 508 ARG 0.006 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASN cc_start: 0.5952 (m-40) cc_final: 0.5710 (p0) REVERT: A 474 MET cc_start: 0.3478 (OUTLIER) cc_final: 0.2980 (tpp) REVERT: C 338 PHE cc_start: 0.3603 (OUTLIER) cc_final: 0.3344 (m-10) REVERT: C 740 MET cc_start: 0.9418 (tmm) cc_final: 0.8991 (tmm) REVERT: C 900 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: C 988 GLU cc_start: 0.9440 (mp0) cc_final: 0.9204 (mp0) REVERT: D 133 PHE cc_start: 0.8068 (m-80) cc_final: 0.7153 (m-80) REVERT: D 900 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8319 (mtp) REVERT: E 123 MET cc_start: 0.1673 (mtm) cc_final: -0.0336 (tpp) REVERT: E 360 MET cc_start: 0.0558 (mtm) cc_final: 0.0190 (mpp) REVERT: E 474 MET cc_start: 0.3069 (mmt) cc_final: 0.2528 (pp-130) REVERT: E 497 TYR cc_start: -0.0007 (m-80) cc_final: -0.0573 (p90) REVERT: E 513 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5578 (tp) REVERT: F 227 GLU cc_start: 0.3546 (mm-30) cc_final: 0.2978 (tm-30) outliers start: 51 outliers final: 16 residues processed: 190 average time/residue: 1.1333 time to fit residues: 268.8758 Evaluate side-chains 156 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 136 optimal weight: 1.9990 chunk 342 optimal weight: 0.0050 chunk 325 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 368 optimal weight: 0.3980 chunk 389 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 424 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 ASN ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.139411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.096244 restraints weight = 272362.036| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 10.35 r_work: 0.3290 rms_B_bonded: 7.63 restraints_weight: 2.0000 r_work: 0.3347 rms_B_bonded: 5.05 restraints_weight: 4.0000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40508 Z= 0.145 Angle : 0.562 11.356 55106 Z= 0.282 Chirality : 0.043 0.394 6279 Planarity : 0.004 0.060 7002 Dihedral : 6.169 54.808 6866 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.89 % Rotamer: Outliers : 1.13 % Allowed : 11.45 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.12), residues: 4775 helix: 1.76 (0.13), residues: 1701 sheet: -0.12 (0.20), residues: 644 loop : -1.58 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 163 HIS 0.003 0.000 HIS A 401 PHE 0.032 0.001 PHE D 515 TYR 0.020 0.001 TYR D 904 ARG 0.005 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASN cc_start: 0.5877 (m-40) cc_final: 0.5674 (p0) REVERT: B 105 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7930 (tp) REVERT: C 740 MET cc_start: 0.9335 (tmm) cc_final: 0.8815 (tmm) REVERT: D 133 PHE cc_start: 0.8740 (m-80) cc_final: 0.7652 (m-80) REVERT: D 214 ARG cc_start: 0.2826 (OUTLIER) cc_final: 0.1755 (mmp-170) REVERT: E 123 MET cc_start: 0.1741 (mtm) cc_final: 0.0598 (tpp) REVERT: E 172 VAL cc_start: 0.4473 (t) cc_final: 0.4187 (p) REVERT: E 474 MET cc_start: 0.3168 (mmt) cc_final: 0.2376 (pp-130) REVERT: E 480 MET cc_start: 0.1684 (ppp) cc_final: 0.1452 (ppp) REVERT: E 497 TYR cc_start: -0.0200 (m-80) cc_final: -0.0663 (p90) REVERT: E 513 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5632 (tp) outliers start: 48 outliers final: 10 residues processed: 183 average time/residue: 1.1976 time to fit residues: 271.7791 Evaluate side-chains 143 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 289 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 460 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 431 optimal weight: 0.0980 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 360 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.134075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.105175 restraints weight = 326125.081| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 8.57 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40508 Z= 0.251 Angle : 0.619 14.478 55106 Z= 0.308 Chirality : 0.044 0.406 6279 Planarity : 0.004 0.064 7002 Dihedral : 6.290 58.918 6866 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 1.27 % Allowed : 12.20 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.12), residues: 4775 helix: 1.65 (0.13), residues: 1713 sheet: -0.29 (0.21), residues: 634 loop : -1.56 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 163 HIS 0.004 0.001 HIS F 374 PHE 0.024 0.001 PHE B 371 TYR 0.027 0.001 TYR D 904 ARG 0.004 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 139 time to evaluate : 3.365 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 250 ASN cc_start: 0.6236 (m-40) cc_final: 0.5865 (p0) REVERT: B 518 LEU cc_start: 0.8446 (tm) cc_final: 0.7764 (pt) REVERT: C 740 MET cc_start: 0.9143 (tmm) cc_final: 0.8611 (tmm) REVERT: D 133 PHE cc_start: 0.8963 (m-80) cc_final: 0.8034 (m-80) REVERT: D 214 ARG cc_start: 0.2780 (OUTLIER) cc_final: 0.1657 (mmp-170) REVERT: E 123 MET cc_start: -0.0586 (mtm) cc_final: -0.0907 (mtm) REVERT: E 228 HIS cc_start: 0.4820 (t-170) cc_final: 0.4346 (m90) REVERT: E 480 MET cc_start: 0.0149 (ppp) cc_final: -0.0168 (ppp) REVERT: F 472 GLN cc_start: 0.5718 (mm-40) cc_final: 0.5487 (tp-100) outliers start: 54 outliers final: 18 residues processed: 186 average time/residue: 1.1482 time to fit residues: 268.8370 Evaluate side-chains 150 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 120 optimal weight: 0.9990 chunk 346 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 368 optimal weight: 6.9990 chunk 275 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.095916 restraints weight = 311727.740| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 11.94 r_work: 0.3239 rms_B_bonded: 7.57 restraints_weight: 2.0000 r_work: 0.3355 rms_B_bonded: 5.85 restraints_weight: 4.0000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40508 Z= 0.185 Angle : 0.591 13.355 55106 Z= 0.293 Chirality : 0.043 0.410 6279 Planarity : 0.004 0.065 7002 Dihedral : 6.159 58.470 6866 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.05 % Favored : 94.80 % Rotamer: Outliers : 1.08 % Allowed : 12.51 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.12), residues: 4775 helix: 1.69 (0.13), residues: 1706 sheet: -0.09 (0.20), residues: 650 loop : -1.56 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 163 HIS 0.006 0.001 HIS E 493 PHE 0.024 0.001 PHE B 371 TYR 0.025 0.001 TYR D 904 ARG 0.006 0.000 ARG F 245 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASN cc_start: 0.6101 (m-40) cc_final: 0.5844 (p0) REVERT: B 518 LEU cc_start: 0.8437 (tm) cc_final: 0.7846 (pt) REVERT: C 740 MET cc_start: 0.9343 (tmm) cc_final: 0.8847 (tmm) REVERT: C 988 GLU cc_start: 0.9156 (mp0) cc_final: 0.8908 (mp0) REVERT: D 133 PHE cc_start: 0.8574 (m-80) cc_final: 0.7488 (m-80) REVERT: D 214 ARG cc_start: 0.2559 (OUTLIER) cc_final: 0.1229 (mmp-170) REVERT: D 988 GLU cc_start: 0.9289 (mp0) cc_final: 0.9079 (mp0) REVERT: E 480 MET cc_start: 0.1429 (ppp) cc_final: 0.1189 (ppp) REVERT: E 513 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6437 (tp) outliers start: 46 outliers final: 19 residues processed: 183 average time/residue: 1.1485 time to fit residues: 261.9068 Evaluate side-chains 152 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 321 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 377 optimal weight: 2.9990 chunk 384 optimal weight: 0.9990 chunk 240 optimal weight: 0.0770 chunk 310 optimal weight: 0.0170 chunk 114 optimal weight: 5.9990 chunk 421 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.138336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.095907 restraints weight = 349677.802| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 14.20 r_work: 0.3201 rms_B_bonded: 7.66 restraints_weight: 2.0000 r_work: 0.3290 rms_B_bonded: 6.22 restraints_weight: 4.0000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40508 Z= 0.195 Angle : 0.599 14.154 55106 Z= 0.297 Chirality : 0.043 0.404 6279 Planarity : 0.004 0.056 7002 Dihedral : 6.104 58.208 6866 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.43 % Favored : 94.43 % Rotamer: Outliers : 1.01 % Allowed : 12.63 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.12), residues: 4775 helix: 1.67 (0.13), residues: 1709 sheet: -0.15 (0.20), residues: 658 loop : -1.52 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 163 HIS 0.009 0.001 HIS E 228 PHE 0.029 0.001 PHE B 371 TYR 0.030 0.001 TYR D 904 ARG 0.004 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 3.451 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 250 ASN cc_start: 0.6102 (m-40) cc_final: 0.5843 (p0) REVERT: C 740 MET cc_start: 0.9378 (tmm) cc_final: 0.8884 (tmm) REVERT: D 214 ARG cc_start: 0.2972 (OUTLIER) cc_final: 0.1602 (mmp-170) REVERT: E 480 MET cc_start: 0.1461 (ppp) cc_final: 0.1254 (ppp) outliers start: 43 outliers final: 24 residues processed: 171 average time/residue: 1.1784 time to fit residues: 251.3202 Evaluate side-chains 153 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 3.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 26 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 355 optimal weight: 1.9990 chunk 448 optimal weight: 0.0570 chunk 276 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 390 optimal weight: 5.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.138540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.086608 restraints weight = 285767.502| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 13.17 r_work: 0.3314 rms_B_bonded: 8.09 restraints_weight: 2.0000 r_work: 0.3363 rms_B_bonded: 5.97 restraints_weight: 4.0000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40508 Z= 0.191 Angle : 0.602 14.642 55106 Z= 0.296 Chirality : 0.043 0.405 6279 Planarity : 0.004 0.053 7002 Dihedral : 6.056 56.819 6866 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 0.87 % Allowed : 12.96 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.12), residues: 4775 helix: 1.67 (0.13), residues: 1709 sheet: -0.14 (0.20), residues: 658 loop : -1.49 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 478 HIS 0.004 0.001 HIS E 493 PHE 0.029 0.001 PHE B 371 TYR 0.030 0.001 TYR D 904 ARG 0.003 0.000 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 3.389 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: C 740 MET cc_start: 0.9403 (tmm) cc_final: 0.8918 (tmm) REVERT: C 900 MET cc_start: 0.8895 (mmm) cc_final: 0.8471 (mtm) REVERT: D 214 ARG cc_start: 0.2330 (OUTLIER) cc_final: 0.1073 (mmp-170) REVERT: E 513 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6189 (tp) outliers start: 37 outliers final: 21 residues processed: 164 average time/residue: 1.1742 time to fit residues: 241.4332 Evaluate side-chains 151 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 448 optimal weight: 0.9990 chunk 379 optimal weight: 5.9990 chunk 232 optimal weight: 0.0270 chunk 276 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 391 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 97 optimal weight: 30.0000 chunk 404 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 180 optimal weight: 0.6980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 524 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.139093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.094417 restraints weight = 276606.617| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 10.80 r_work: 0.3273 rms_B_bonded: 7.62 restraints_weight: 2.0000 r_work: 0.3349 rms_B_bonded: 5.85 restraints_weight: 4.0000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 40508 Z= 0.149 Angle : 0.597 15.244 55106 Z= 0.292 Chirality : 0.043 0.386 6279 Planarity : 0.004 0.053 7002 Dihedral : 5.916 58.433 6866 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 0.54 % Allowed : 13.45 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.12), residues: 4775 helix: 1.75 (0.13), residues: 1702 sheet: -0.12 (0.20), residues: 656 loop : -1.41 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 478 HIS 0.006 0.001 HIS B 519 PHE 0.032 0.001 PHE B 371 TYR 0.032 0.001 TYR D 904 ARG 0.004 0.000 ARG F 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.6703 (mpm) cc_final: 0.6236 (pmm) REVERT: A 171 GLU cc_start: 0.3869 (OUTLIER) cc_final: 0.3445 (tt0) REVERT: C 740 MET cc_start: 0.9357 (tmm) cc_final: 0.8836 (tmm) REVERT: C 900 MET cc_start: 0.8809 (mmm) cc_final: 0.8490 (mtm) REVERT: D 214 ARG cc_start: 0.3494 (OUTLIER) cc_final: 0.2380 (mmp-170) REVERT: D 900 MET cc_start: 0.8611 (mmm) cc_final: 0.8251 (mtm) REVERT: E 332 MET cc_start: 0.2318 (OUTLIER) cc_final: 0.1304 (mtm) REVERT: E 480 MET cc_start: 0.0699 (ppp) cc_final: -0.0047 (tpp) REVERT: E 513 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6280 (tp) outliers start: 23 outliers final: 11 residues processed: 157 average time/residue: 1.2195 time to fit residues: 238.2408 Evaluate side-chains 144 residues out of total 4239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 187 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 400 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 0.0050 chunk 370 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 342 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.135987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.104987 restraints weight = 300629.790| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 6.82 r_work: 0.3458 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40508 Z= 0.209 Angle : 0.631 20.337 55106 Z= 0.308 Chirality : 0.043 0.396 6279 Planarity : 0.004 0.055 7002 Dihedral : 5.991 55.271 6866 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 0.49 % Allowed : 13.57 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.12), residues: 4775 helix: 1.64 (0.13), residues: 1706 sheet: -0.06 (0.20), residues: 653 loop : -1.43 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 478 HIS 0.005 0.001 HIS E 378 PHE 0.018 0.001 PHE B1089 TYR 0.033 0.001 TYR D 904 ARG 0.003 0.000 ARG F 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 75448.25 seconds wall clock time: 1278 minutes 4.48 seconds (76684.48 seconds total)