Starting phenix.real_space_refine on Thu Oct 10 12:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_38826.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_38826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_38826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_38826.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y16_38826/10_2024/8y16_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 21.59, 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: 8.03 Conformation dependent library (CDL) restraints added in 4.7 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: 3.98 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: 14.59 Time building geometry restraints manager: 9.38 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: 7.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 83.080 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.270 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:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.390 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 327 time to evaluate : 3.327 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: 1.2209 time to fit residues: 492.8553 Evaluate side-chains 157 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 3.283 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4705 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 fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: -0.0056 (mmm) cc_final: -0.0781 (mtp) REVERT: E 123 MET cc_start: 0.0715 (mtm) cc_final: -0.2485 (tpp) REVERT: E 142 LEU cc_start: 0.3844 (pp) cc_final: 0.3169 (mm) REVERT: E 376 MET cc_start: 0.5687 (tpt) cc_final: 0.3678 (mtt) REVERT: F 245 ARG cc_start: 0.2817 (OUTLIER) cc_final: 0.2597 (ptp90) REVERT: F 408 MET cc_start: -0.0824 (mmt) cc_final: -0.1059 (mtt) outliers start: 35 outliers final: 10 residues processed: 201 average time/residue: 1.2320 time to fit residues: 303.6528 Evaluate side-chains 145 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 245 ARG 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 241 optimal weight: 0.0030 chunk 135 optimal weight: 0.5980 chunk 362 optimal weight: 7.9990 chunk 296 optimal weight: 50.0000 chunk 119 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 470 optimal weight: 20.0000 chunk 388 optimal weight: 0.0370 chunk 432 optimal weight: 0.0980 chunk 148 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 overall best weight: 0.9470 ------------------------------------------------------------------------------- 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 ** D 439 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 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4706 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40508 Z= 0.163 Angle : 0.586 16.445 55106 Z= 0.292 Chirality : 0.044 0.385 6279 Planarity : 0.004 0.060 7002 Dihedral : 7.255 58.994 6866 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.87 % Rotamer: Outliers : 0.97 % Allowed : 8.79 % Favored : 90.25 % 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: -0.22 (0.12), residues: 4775 helix: 1.84 (0.13), residues: 1679 sheet: -0.06 (0.21), residues: 609 loop : -1.66 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 275 HIS 0.008 0.001 HIS F 540 PHE 0.030 0.001 PHE E 438 TYR 0.019 0.001 TYR E 497 ARG 0.009 0.000 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 fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: -0.0130 (mmm) cc_final: -0.1007 (mtp) REVERT: A 474 MET cc_start: -0.1174 (OUTLIER) cc_final: -0.3137 (pmm) REVERT: D 133 PHE cc_start: 0.6749 (m-10) cc_final: 0.6539 (m-80) REVERT: D 214 ARG cc_start: 0.2008 (OUTLIER) cc_final: 0.1265 (mmp-170) REVERT: E 123 MET cc_start: 0.0765 (mtm) cc_final: -0.2412 (tpp) REVERT: E 142 LEU cc_start: 0.3776 (pp) cc_final: 0.3382 (mm) REVERT: E 245 ARG cc_start: 0.2662 (OUTLIER) cc_final: 0.2406 (ttm110) REVERT: E 360 MET cc_start: 0.3009 (OUTLIER) cc_final: 0.2794 (mtm) REVERT: E 513 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.2888 (tp) REVERT: F 245 ARG cc_start: 0.2739 (OUTLIER) cc_final: 0.2514 (ptp90) REVERT: F 462 MET cc_start: -0.1400 (mtp) cc_final: -0.1648 (mtt) outliers start: 41 outliers final: 10 residues processed: 181 average time/residue: 1.2393 time to fit residues: 275.2273 Evaluate side-chains 149 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 360 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 245 ARG 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 430 optimal weight: 30.0000 chunk 327 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 207 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 437 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 228 optimal weight: 6.9990 chunk 414 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** ** 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** ** E 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4789 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 40508 Z= 0.254 Angle : 0.621 11.940 55106 Z= 0.309 Chirality : 0.045 0.469 6279 Planarity : 0.004 0.061 7002 Dihedral : 6.588 58.290 6866 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 1.37 % Allowed : 10.22 % Favored : 88.41 % 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: -0.29 (0.12), residues: 4775 helix: 1.68 (0.13), residues: 1697 sheet: -0.31 (0.21), residues: 625 loop : -1.59 (0.12), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 275 HIS 0.004 0.001 HIS D1083 PHE 0.019 0.001 PHE D1089 TYR 0.024 0.001 TYR C 508 ARG 0.006 0.000 ARG D 567 *********************** 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 198 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 140 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.0042 (mmm) cc_final: -0.1089 (mtp) REVERT: D 133 PHE cc_start: 0.7092 (m-80) cc_final: 0.6797 (m-80) REVERT: E 123 MET cc_start: 0.0824 (mtm) cc_final: -0.2408 (tpp) REVERT: E 142 LEU cc_start: 0.3839 (pp) cc_final: 0.3374 (mm) REVERT: E 323 MET cc_start: 0.0970 (OUTLIER) cc_final: 0.0130 (tpp) REVERT: E 360 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2903 (mtm) REVERT: E 513 ILE cc_start: 0.3444 (OUTLIER) cc_final: 0.2932 (tp) REVERT: F 245 ARG cc_start: 0.2717 (OUTLIER) cc_final: 0.2473 (ptp90) REVERT: F 462 MET cc_start: -0.1259 (mtp) cc_final: -0.1491 (mtt) outliers start: 58 outliers final: 18 residues processed: 185 average time/residue: 1.1797 time to fit residues: 271.0559 Evaluate side-chains 154 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1010 GLN 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 E residue 59 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 360 MET 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 245 ARG Chi-restraints excluded: chain F residue 341 LYS 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 385 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 191 optimal weight: 50.0000 chunk 395 optimal weight: 0.9990 chunk 320 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 0.6980 chunk 415 optimal weight: 6.9990 chunk 116 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 472 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4755 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40508 Z= 0.155 Angle : 0.569 12.424 55106 Z= 0.284 Chirality : 0.043 0.398 6279 Planarity : 0.004 0.060 7002 Dihedral : 6.220 58.582 6866 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 1.15 % Allowed : 11.40 % Favored : 87.44 % 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: 1.77 (0.13), residues: 1698 sheet: -0.15 (0.20), residues: 646 loop : -1.59 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 163 HIS 0.003 0.001 HIS A 401 PHE 0.033 0.001 PHE D 515 TYR 0.019 0.001 TYR E 50 ARG 0.005 0.000 ARG F 482 *********************** 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 192 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 3.257 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: 0.0175 (mmm) cc_final: -0.0999 (mtp) REVERT: D 133 PHE cc_start: 0.6958 (m-80) cc_final: 0.6676 (m-80) REVERT: D 214 ARG cc_start: 0.2125 (OUTLIER) cc_final: 0.1219 (mmp-170) REVERT: E 57 GLU cc_start: 0.1871 (OUTLIER) cc_final: 0.0064 (pm20) REVERT: E 123 MET cc_start: 0.0825 (mtm) cc_final: -0.2415 (tpp) REVERT: E 142 LEU cc_start: 0.3786 (pp) cc_final: 0.3302 (mm) REVERT: E 480 MET cc_start: -0.0204 (ppp) cc_final: -0.3298 (tpp) REVERT: E 513 ILE cc_start: 0.3444 (OUTLIER) cc_final: 0.3034 (tp) REVERT: F 227 GLU cc_start: 0.2080 (mm-30) cc_final: 0.1629 (tm-30) REVERT: F 245 ARG cc_start: 0.2641 (OUTLIER) cc_final: 0.2398 (ptp90) REVERT: F 408 MET cc_start: 0.0357 (mtt) cc_final: 0.0117 (ptp) REVERT: F 472 GLN cc_start: 0.4531 (OUTLIER) cc_final: 0.3907 (mm110) outliers start: 49 outliers final: 13 residues processed: 179 average time/residue: 1.2197 time to fit residues: 271.3327 Evaluate side-chains 150 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 858 LEU 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 638 THR Chi-restraints excluded: chain E residue 57 GLU 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 245 ARG Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 472 GLN 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 155 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 463 optimal weight: 9.9990 chunk 384 optimal weight: 0.4980 chunk 214 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 243 optimal weight: 6.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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 901 GLN B 914 ASN B 919 ASN C 115 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C1071 GLN C1125 ASN D 188 ASN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** D 641 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** E 580 ASN F 194 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 HIS ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4930 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 40508 Z= 0.500 Angle : 0.810 13.754 55106 Z= 0.405 Chirality : 0.049 0.505 6279 Planarity : 0.005 0.071 7002 Dihedral : 6.991 59.850 6866 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.11 % Rotamer: Outliers : 1.72 % Allowed : 11.87 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.77 (0.12), residues: 4775 helix: 1.10 (0.12), residues: 1679 sheet: -0.51 (0.20), residues: 660 loop : -1.73 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 473 HIS 0.008 0.002 HIS E 265 PHE 0.035 0.003 PHE D1089 TYR 0.038 0.002 TYR D 904 ARG 0.009 0.001 ARG B 905 *********************** 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 213 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 140 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.0312 (mmm) cc_final: -0.0792 (mtp) REVERT: C 191 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: C 1116 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8618 (p) REVERT: D 214 ARG cc_start: 0.2028 (OUTLIER) cc_final: 0.0204 (mmp-170) REVERT: E 57 GLU cc_start: 0.1772 (OUTLIER) cc_final: 0.0263 (pm20) REVERT: E 150 GLU cc_start: 0.1972 (OUTLIER) cc_final: -0.0691 (mp0) REVERT: E 199 TYR cc_start: 0.1963 (OUTLIER) cc_final: 0.1530 (m-80) REVERT: F 245 ARG cc_start: 0.2745 (OUTLIER) cc_final: 0.2140 (ttp-110) REVERT: F 341 LYS cc_start: 0.0956 (OUTLIER) cc_final: -0.0203 (pttm) REVERT: F 408 MET cc_start: 0.0906 (mtt) cc_final: 0.0329 (mtm) REVERT: F 472 GLN cc_start: 0.4673 (OUTLIER) cc_final: 0.3664 (mm-40) outliers start: 73 outliers final: 21 residues processed: 200 average time/residue: 1.1604 time to fit residues: 288.3606 Evaluate side-chains 157 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 191 GLU 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 858 LEU 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 191 GLU 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 57 GLU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 245 ARG Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 472 GLN 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 446 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 264 optimal weight: 3.9990 chunk 338 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 390 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 chunk 461 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 281 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 901 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** 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 42 GLN F 472 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4853 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40508 Z= 0.211 Angle : 0.622 14.468 55106 Z= 0.309 Chirality : 0.044 0.450 6279 Planarity : 0.004 0.069 7002 Dihedral : 6.521 57.331 6866 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.39 % Favored : 94.47 % Rotamer: Outliers : 1.11 % Allowed : 12.77 % Favored : 86.12 % 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: -0.41 (0.12), residues: 4775 helix: 1.46 (0.13), residues: 1696 sheet: -0.21 (0.20), residues: 676 loop : -1.63 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 163 HIS 0.009 0.001 HIS E 228 PHE 0.022 0.001 PHE D 515 TYR 0.024 0.001 TYR D 904 ARG 0.004 0.000 ARG F 482 *********************** 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 183 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5077 (mpm) cc_final: 0.3891 (pmm) REVERT: A 297 MET cc_start: 0.0237 (mmm) cc_final: -0.0889 (mtp) REVERT: A 366 MET cc_start: 0.4588 (tpp) cc_final: 0.3749 (tpt) REVERT: D 214 ARG cc_start: 0.2025 (OUTLIER) cc_final: 0.0350 (mmp-170) REVERT: E 57 GLU cc_start: 0.1693 (OUTLIER) cc_final: 0.0446 (pm20) REVERT: E 142 LEU cc_start: 0.4498 (pp) cc_final: 0.3463 (mm) REVERT: E 480 MET cc_start: -0.0612 (ppp) cc_final: -0.3326 (tpp) REVERT: E 579 MET cc_start: 0.2473 (OUTLIER) cc_final: 0.1947 (ptp) REVERT: F 123 MET cc_start: -0.1814 (mmt) cc_final: -0.3827 (tmm) REVERT: F 270 MET cc_start: 0.3914 (tpp) cc_final: 0.3462 (tmt) REVERT: F 341 LYS cc_start: 0.0799 (OUTLIER) cc_final: -0.0338 (pttm) REVERT: F 383 MET cc_start: 0.1909 (mmm) cc_final: 0.1242 (mmm) REVERT: F 408 MET cc_start: 0.0747 (mtt) cc_final: 0.0199 (mtm) REVERT: F 472 GLN cc_start: 0.4993 (OUTLIER) cc_final: 0.3744 (mm-40) outliers start: 47 outliers final: 18 residues processed: 178 average time/residue: 1.1824 time to fit residues: 262.0439 Evaluate side-chains 152 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 858 LEU 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 E residue 57 GLU 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 519 THR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 472 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 285 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 275 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 293 optimal weight: 30.0000 chunk 314 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 362 optimal weight: 30.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN ** 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 239 HIS F 472 GLN ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4882 moved from start: 0.3971 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= 0.279 Angle : 0.646 14.495 55106 Z= 0.320 Chirality : 0.045 0.449 6279 Planarity : 0.004 0.068 7002 Dihedral : 6.510 57.592 6866 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.99 % Favored : 93.86 % Rotamer: Outliers : 1.15 % Allowed : 12.86 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.46 (0.12), residues: 4775 helix: 1.41 (0.13), residues: 1703 sheet: -0.35 (0.20), residues: 635 loop : -1.61 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 473 HIS 0.004 0.001 HIS E 265 PHE 0.019 0.001 PHE F 592 TYR 0.079 0.001 TYR A 613 ARG 0.007 0.000 ARG F 245 *********************** 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 fitting. rotamer outliers: 49 poor density : 126 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.0102 (mmm) cc_final: -0.0961 (mtp) REVERT: A 366 MET cc_start: 0.4451 (tpp) cc_final: 0.3618 (tpt) REVERT: D 214 ARG cc_start: 0.1967 (OUTLIER) cc_final: 0.0193 (mmp-170) REVERT: E 57 GLU cc_start: 0.1767 (OUTLIER) cc_final: 0.0471 (pm20) REVERT: E 142 LEU cc_start: 0.4633 (pp) cc_final: 0.3510 (mm) REVERT: E 150 GLU cc_start: 0.2001 (OUTLIER) cc_final: -0.0721 (mp0) REVERT: E 480 MET cc_start: -0.0637 (ppp) cc_final: -0.3346 (tpp) REVERT: F 123 MET cc_start: -0.1761 (OUTLIER) cc_final: -0.3771 (tmm) REVERT: F 270 MET cc_start: 0.3981 (tpp) cc_final: 0.3586 (tmt) REVERT: F 341 LYS cc_start: 0.0941 (OUTLIER) cc_final: -0.0207 (pttm) REVERT: F 408 MET cc_start: 0.0820 (mtt) cc_final: 0.0244 (mtm) REVERT: F 472 GLN cc_start: 0.4986 (OUTLIER) cc_final: 0.3977 (mm110) outliers start: 49 outliers final: 24 residues processed: 167 average time/residue: 1.2090 time to fit residues: 251.0350 Evaluate side-chains 156 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 3.430 ------------------------------------------------------------------------------- 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 523 THR Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 191 GLU 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 660 TYR Chi-restraints excluded: chain C residue 858 LEU 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 501 TYR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 57 GLU 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 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 341 LYS Chi-restraints excluded: chain F residue 472 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 9.9990 chunk 442 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 430 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 337 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 406 optimal weight: 5.9990 chunk 428 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 487 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4885 moved from start: 0.4229 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= 0.263 Angle : 0.642 14.666 55106 Z= 0.318 Chirality : 0.044 0.448 6279 Planarity : 0.004 0.060 7002 Dihedral : 6.475 58.388 6866 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 1.15 % Allowed : 13.05 % Favored : 85.80 % 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: -0.46 (0.12), residues: 4775 helix: 1.39 (0.13), residues: 1705 sheet: -0.31 (0.20), residues: 670 loop : -1.62 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 478 HIS 0.008 0.001 HIS B 519 PHE 0.019 0.001 PHE B 371 TYR 0.034 0.001 TYR D 904 ARG 0.007 0.000 ARG F 245 *********************** 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 179 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5389 (mpm) cc_final: 0.3985 (pmm) REVERT: A 297 MET cc_start: 0.0105 (mmm) cc_final: -0.0984 (mtp) REVERT: A 366 MET cc_start: 0.4395 (tpp) cc_final: 0.3550 (tpt) REVERT: B 492 LEU cc_start: 0.4747 (tp) cc_final: 0.4494 (tp) REVERT: D 214 ARG cc_start: 0.1839 (OUTLIER) cc_final: 0.0002 (mmp-170) REVERT: E 150 GLU cc_start: 0.2024 (OUTLIER) cc_final: -0.0702 (mp0) REVERT: E 383 MET cc_start: 0.1550 (mtp) cc_final: 0.0946 (mpt) REVERT: E 480 MET cc_start: -0.0438 (ppp) cc_final: -0.3150 (tpp) REVERT: F 123 MET cc_start: -0.1744 (OUTLIER) cc_final: -0.3729 (tmm) REVERT: F 190 MET cc_start: 0.0440 (ttt) cc_final: 0.0027 (pp-130) REVERT: F 270 MET cc_start: 0.4155 (tpp) cc_final: 0.3925 (tmt) REVERT: F 341 LYS cc_start: 0.1119 (OUTLIER) cc_final: -0.0051 (pttm) REVERT: F 408 MET cc_start: 0.0807 (mtt) cc_final: 0.0229 (mtm) outliers start: 49 outliers final: 27 residues processed: 173 average time/residue: 1.1879 time to fit residues: 255.4776 Evaluate side-chains 156 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 3.259 ------------------------------------------------------------------------------- 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 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE 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 332 VAL Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 882 ILE Chi-restraints excluded: chain D residue 1104 VAL 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 507 SER Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 519 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 341 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 282 optimal weight: 3.9990 chunk 454 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 477 optimal weight: 9.9990 chunk 439 optimal weight: 30.0000 chunk 380 optimal weight: 30.0000 chunk 39 optimal weight: 0.4980 chunk 293 optimal weight: 30.0000 chunk 233 optimal weight: 4.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 544 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4924 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 40508 Z= 0.337 Angle : 0.688 13.623 55106 Z= 0.341 Chirality : 0.046 0.472 6279 Planarity : 0.004 0.072 7002 Dihedral : 6.653 59.409 6866 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.99 % Allowed : 13.31 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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: -0.60 (0.12), residues: 4775 helix: 1.28 (0.13), residues: 1693 sheet: -0.57 (0.20), residues: 667 loop : -1.63 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 478 HIS 0.009 0.001 HIS C 519 PHE 0.026 0.002 PHE B 371 TYR 0.033 0.002 TYR D 904 ARG 0.016 0.001 ARG C 357 ********************** 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 166 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.1130 (mtt) cc_final: 0.0712 (mtt) REVERT: A 297 MET cc_start: 0.0195 (mmm) cc_final: -0.0807 (mtp) REVERT: A 366 MET cc_start: 0.4412 (tpp) cc_final: 0.3617 (tpt) REVERT: C 191 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: D 214 ARG cc_start: 0.1744 (OUTLIER) cc_final: -0.0263 (mmp-170) REVERT: E 150 GLU cc_start: 0.2066 (OUTLIER) cc_final: -0.0676 (mp0) REVERT: E 480 MET cc_start: -0.0285 (ppp) cc_final: -0.3007 (tpp) REVERT: F 123 MET cc_start: -0.1636 (OUTLIER) cc_final: -0.3644 (tmm) REVERT: F 190 MET cc_start: 0.0530 (ttt) cc_final: -0.0169 (pp-130) REVERT: F 270 MET cc_start: 0.4396 (tpp) cc_final: 0.3965 (tmt) REVERT: F 341 LYS cc_start: 0.1198 (OUTLIER) cc_final: -0.0060 (pttm) REVERT: F 408 MET cc_start: 0.0937 (mtt) cc_final: 0.0392 (mtm) outliers start: 42 outliers final: 26 residues processed: 163 average time/residue: 1.1757 time to fit residues: 240.1517 Evaluate side-chains 151 residues out of total 4239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 613 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 191 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 931 ILE 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 332 VAL 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 150 GLU 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 519 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 341 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 301 optimal weight: 30.0000 chunk 404 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 105 optimal weight: 0.0170 chunk 380 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 390 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.2102 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 544 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.137081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.090928 restraints weight = 293592.514| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 11.98 r_work: 0.3235 rms_B_bonded: 7.66 restraints_weight: 2.0000 r_work: 0.3313 rms_B_bonded: 6.05 restraints_weight: 4.0000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40508 Z= 0.226 Angle : 0.643 13.762 55106 Z= 0.318 Chirality : 0.044 0.454 6279 Planarity : 0.004 0.061 7002 Dihedral : 6.517 56.265 6866 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 0.94 % Allowed : 13.38 % Favored : 85.68 % 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: -0.53 (0.12), residues: 4775 helix: 1.28 (0.13), residues: 1720 sheet: -0.40 (0.20), residues: 682 loop : -1.63 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 478 HIS 0.005 0.001 HIS F 401 PHE 0.018 0.001 PHE F 592 TYR 0.033 0.001 TYR D 904 ARG 0.005 0.000 ARG F 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13495.41 seconds wall clock time: 234 minutes 12.10 seconds (14052.10 seconds total)