Starting phenix.real_space_refine on Tue Nov 19 15:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvm_38690/11_2024/8xvm_38690.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 14628 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 25455 2.51 5 N 6486 2.21 5 O 7716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 39852 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8056 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 6 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8056 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 8056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8056 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 55, 'TRANS': 972} Chain breaks: 6 Chain: "L" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 21.42, per 1000 atoms: 0.54 Number of scatterers: 39852 At special positions: 0 Unit cell: (163.815, 160.8, 231.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7716 8.00 N 6486 7.00 C 25455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.04 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.04 Simple disulfide: pdb=" SG CYS K 290 " - pdb=" SG CYS K 300 " distance=2.03 Simple disulfide: pdb=" SG CYS K 335 " - pdb=" SG CYS K 360 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 431 " distance=2.03 Simple disulfide: pdb=" SG CYS K 390 " - pdb=" SG CYS K 523 " distance=2.03 Simple disulfide: pdb=" SG CYS K 479 " - pdb=" SG CYS K 486 " distance=2.03 Simple disulfide: pdb=" SG CYS K 536 " - pdb=" SG CYS K 588 " distance=2.03 Simple disulfide: pdb=" SG CYS K 615 " - pdb=" SG CYS K 647 " distance=2.03 Simple disulfide: pdb=" SG CYS K 660 " - pdb=" SG CYS K 669 " distance=2.03 Simple disulfide: pdb=" SG CYS K 736 " - pdb=" SG CYS K 758 " distance=2.03 Simple disulfide: pdb=" SG CYS K 741 " - pdb=" SG CYS K 747 " distance=2.03 Simple disulfide: pdb=" SG CYS K1030 " - pdb=" SG CYS K1041 " distance=2.03 Simple disulfide: pdb=" SG CYS K1080 " - pdb=" SG CYS K1124 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 141 " distance=2.04 Simple disulfide: pdb=" SG CYS L 344 " - pdb=" SG CYS L 361 " distance=2.03 Simple disulfide: pdb=" SG CYS L 530 " - pdb=" SG CYS L 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 233 " " NAG A1305 " - " ASN A 281 " " NAG A1306 " - " ASN A 614 " " NAG A1307 " - " ASN A 655 " " NAG A1308 " - " ASN A 707 " " NAG A1309 " - " ASN A1072 " " NAG A1310 " - " ASN A1096 " " NAG A1311 " - " ASN A1132 " " NAG A1312 " - " ASN A 330 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 233 " " NAG B1305 " - " ASN B 281 " " NAG B1306 " - " ASN B 614 " " NAG B1307 " - " ASN B 655 " " NAG B1308 " - " ASN B 707 " " NAG B1309 " - " ASN B1072 " " NAG B1310 " - " ASN B1096 " " NAG B1311 " - " ASN B1132 " " NAG B1312 " - " ASN B 330 " " NAG C 701 " - " ASN C 322 " " NAG C 702 " - " ASN C 432 " " NAG C 703 " - " ASN C 53 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG E 1 " - " ASN A 715 " " NAG F 1 " - " ASN A 799 " " NAG G 1 " - " ASN B 715 " " NAG H 1 " - " ASN B 799 " " NAG I 1 " - " ASN C 90 " " NAG J 1 " - " ASN C 103 " " NAG K1301 " - " ASN K 61 " " NAG K1302 " - " ASN K 122 " " NAG K1303 " - " ASN K 165 " " NAG K1304 " - " ASN K 233 " " NAG K1305 " - " ASN K 281 " " NAG K1306 " - " ASN K 614 " " NAG K1307 " - " ASN K 655 " " NAG K1308 " - " ASN K 707 " " NAG K1309 " - " ASN K1072 " " NAG K1310 " - " ASN K1096 " " NAG K1311 " - " ASN K1132 " " NAG K1312 " - " ASN K 330 " " NAG L 701 " - " ASN L 322 " " NAG L 702 " - " ASN L 432 " " NAG L 703 " - " ASN L 53 " " NAG M 1 " - " ASN D 90 " " NAG N 1 " - " ASN D 103 " " NAG O 1 " - " ASN K 715 " " NAG P 1 " - " ASN K 799 " " NAG Q 1 " - " ASN L 90 " " NAG R 1 " - " ASN L 103 " Time building additional restraints: 10.13 Conformation dependent library (CDL) restraints added in 5.1 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9162 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 66 sheets defined 41.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.757A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.030A pdb=" N ASN A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.979A pdb=" N SER A 442 " --> pdb=" O LYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.619A pdb=" N VAL A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.642A pdb=" N SER A 748 " --> pdb=" O SER A 744 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.594A pdb=" N ASP A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.650A pdb=" N THR A 825 " --> pdb=" O PHE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.577A pdb=" N GLY A 887 " --> pdb=" O TRP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.593A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.755A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.624A pdb=" N ASN A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 981 removed outlier: 3.732A pdb=" N ARG A 981 " --> pdb=" O ASP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 3.894A pdb=" N GLU A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.575A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.534A pdb=" N GLY D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.561A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 250 removed outlier: 3.869A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.958A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 292 through 300 removed outlier: 4.039A pdb=" N ALA D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 383 Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 414 removed outlier: 4.125A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.709A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 509 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.535A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.636A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 4.128A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.676A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.756A pdb=" N TYR B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.029A pdb=" N ASN B 387 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.979A pdb=" N SER B 442 " --> pdb=" O LYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 3.619A pdb=" N VAL B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.641A pdb=" N SER B 748 " --> pdb=" O SER B 744 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 781 removed outlier: 3.594A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR B 776 " --> pdb=" O GLN B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 825 removed outlier: 3.649A pdb=" N THR B 825 " --> pdb=" O PHE B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 882 Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.577A pdb=" N GLY B 887 " --> pdb=" O TRP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.593A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.755A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 939 " --> pdb=" O SER B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.624A pdb=" N ASN B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 981 removed outlier: 3.732A pdb=" N ARG B 981 " --> pdb=" O ASP B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 3.893A pdb=" N GLU B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.575A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 92 through 104 removed outlier: 3.534A pdb=" N GLY C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 129 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'C' and resid 157 through 194 removed outlier: 3.561A pdb=" N LYS C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 250 removed outlier: 3.869A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.958A pdb=" N ASN C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 292 through 300 removed outlier: 4.039A pdb=" N ALA C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 324 through 331 Processing helix chain 'C' and resid 365 through 383 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 389 through 393 Processing helix chain 'C' and resid 397 through 414 removed outlier: 4.125A pdb=" N HIS C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.709A pdb=" N LEU C 418 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 509 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.535A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.636A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 564 removed outlier: 4.129A pdb=" N GLU C 564 " --> pdb=" O GLY C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 575 removed outlier: 3.676A pdb=" N VAL C 573 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'K' and resid 293 through 303 Processing helix chain 'K' and resid 337 through 341 Processing helix chain 'K' and resid 364 through 369 removed outlier: 3.756A pdb=" N TYR K 368 " --> pdb=" O TYR K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 388 removed outlier: 4.029A pdb=" N ASN K 387 " --> pdb=" O THR K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 409 Processing helix chain 'K' and resid 416 through 421 Processing helix chain 'K' and resid 438 through 442 removed outlier: 3.978A pdb=" N SER K 442 " --> pdb=" O LYS K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 614 through 624 removed outlier: 3.619A pdb=" N VAL K 618 " --> pdb=" O ASN K 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 735 through 741 Processing helix chain 'K' and resid 744 through 753 removed outlier: 3.642A pdb=" N SER K 748 " --> pdb=" O SER K 744 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN K 753 " --> pdb=" O ASN K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 781 removed outlier: 3.594A pdb=" N ASP K 773 " --> pdb=" O ALA K 769 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 776 " --> pdb=" O GLN K 772 " (cutoff:3.500A) Processing helix chain 'K' and resid 814 through 825 removed outlier: 3.649A pdb=" N THR K 825 " --> pdb=" O PHE K 821 " (cutoff:3.500A) Processing helix chain 'K' and resid 864 through 882 Processing helix chain 'K' and resid 884 through 888 removed outlier: 3.578A pdb=" N GLY K 887 " --> pdb=" O TRP K 884 " (cutoff:3.500A) Processing helix chain 'K' and resid 895 through 906 Processing helix chain 'K' and resid 911 through 917 removed outlier: 3.593A pdb=" N TYR K 915 " --> pdb=" O GLN K 911 " (cutoff:3.500A) Processing helix chain 'K' and resid 917 through 939 removed outlier: 3.755A pdb=" N ILE K 932 " --> pdb=" O ALA K 928 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN K 933 " --> pdb=" O ILE K 929 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP K 934 " --> pdb=" O GLY K 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR K 939 " --> pdb=" O SER K 935 " (cutoff:3.500A) Processing helix chain 'K' and resid 940 through 942 No H-bonds generated for 'chain 'K' and resid 940 through 942' Processing helix chain 'K' and resid 943 through 963 removed outlier: 3.624A pdb=" N ASN K 953 " --> pdb=" O VAL K 949 " (cutoff:3.500A) Processing helix chain 'K' and resid 964 through 966 No H-bonds generated for 'chain 'K' and resid 964 through 966' Processing helix chain 'K' and resid 974 through 981 removed outlier: 3.732A pdb=" N ARG K 981 " --> pdb=" O ASP K 977 " (cutoff:3.500A) Processing helix chain 'K' and resid 983 through 1031 removed outlier: 3.893A pdb=" N GLU K 988 " --> pdb=" O PRO K 984 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL K 989 " --> pdb=" O PRO K 985 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN K 990 " --> pdb=" O GLU K 986 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 53 removed outlier: 3.576A pdb=" N ASP L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 80 Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 92 through 104 removed outlier: 3.534A pdb=" N GLY L 104 " --> pdb=" O LEU L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 129 Processing helix chain 'L' and resid 147 through 155 Processing helix chain 'L' and resid 157 through 194 removed outlier: 3.561A pdb=" N LYS L 174 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN L 175 " --> pdb=" O GLU L 171 " (cutoff:3.500A) Proline residue: L 178 - end of helix Processing helix chain 'L' and resid 198 through 205 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 220 through 250 removed outlier: 3.869A pdb=" N GLU L 224 " --> pdb=" O GLY L 220 " (cutoff:3.500A) Proline residue: L 235 - end of helix removed outlier: 3.957A pdb=" N ASN L 250 " --> pdb=" O ALA L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 275 through 279 Processing helix chain 'L' and resid 292 through 300 removed outlier: 4.039A pdb=" N ALA L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 318 Processing helix chain 'L' and resid 324 through 331 Processing helix chain 'L' and resid 365 through 383 Processing helix chain 'L' and resid 384 through 386 No H-bonds generated for 'chain 'L' and resid 384 through 386' Processing helix chain 'L' and resid 389 through 393 Processing helix chain 'L' and resid 397 through 414 removed outlier: 4.125A pdb=" N HIS L 401 " --> pdb=" O ASN L 397 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU L 402 " --> pdb=" O GLU L 398 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N MET L 408 " --> pdb=" O VAL L 404 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR L 414 " --> pdb=" O LEU L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 422 removed outlier: 3.709A pdb=" N LEU L 418 " --> pdb=" O THR L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 447 Processing helix chain 'L' and resid 449 through 466 Processing helix chain 'L' and resid 469 through 471 No H-bonds generated for 'chain 'L' and resid 469 through 471' Processing helix chain 'L' and resid 472 through 484 Processing helix chain 'L' and resid 499 through 502 Processing helix chain 'L' and resid 503 through 509 Processing helix chain 'L' and resid 513 through 533 removed outlier: 3.534A pdb=" N LEU L 520 " --> pdb=" O TYR L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 547 through 559 removed outlier: 3.636A pdb=" N GLY L 551 " --> pdb=" O SER L 547 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET L 557 " --> pdb=" O LYS L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 560 through 564 removed outlier: 4.128A pdb=" N GLU L 564 " --> pdb=" O GLY L 561 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 575 removed outlier: 3.676A pdb=" N VAL L 573 " --> pdb=" O ALA L 569 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 588 Processing helix chain 'L' and resid 588 through 599 Processing sheet with id=1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.204A pdb=" N VAL A 36 " --> pdb=" O LEU A 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.959A pdb=" N ASP A 286 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.516A pdb=" N LEU A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=6, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.631A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 120 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.806A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=9, first strand: chain 'A' and resid 310 through 318 removed outlier: 6.809A pdb=" N VAL A 593 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN A 316 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 591 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=11, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.504A pdb=" N LYS A 377 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=13, first strand: chain 'A' and resid 472 through 473 removed outlier: 3.943A pdb=" N TYR A 487 " --> pdb=" O TYR A 472 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.621A pdb=" N ILE A 585 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.405A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=17, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.505A pdb=" N SER A 719 " --> pdb=" O THR A1064 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.656A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'A' and resid 1118 through 1119 Processing sheet with id=20, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=21, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.657A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.083A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'B' and resid 29 through 30 Processing sheet with id=24, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.203A pdb=" N VAL B 36 " --> pdb=" O LEU B 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.959A pdb=" N ASP B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'B' and resid 227 through 229 removed outlier: 3.516A pdb=" N LEU B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'B' and resid 104 through 107 Processing sheet with id=28, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.631A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 120 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.806A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=31, first strand: chain 'B' and resid 310 through 318 removed outlier: 6.809A pdb=" N VAL B 593 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN B 316 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY B 591 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=33, first strand: chain 'B' and resid 377 through 378 removed outlier: 3.505A pdb=" N LYS B 377 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'B' and resid 451 through 453 Processing sheet with id=35, first strand: chain 'B' and resid 472 through 473 removed outlier: 3.943A pdb=" N TYR B 487 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.621A pdb=" N ILE B 585 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.405A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'B' and resid 709 through 711 Processing sheet with id=39, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.505A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.657A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'B' and resid 1118 through 1119 Processing sheet with id=42, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=43, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.657A pdb=" N VAL C 132 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=43 Processing sheet with id=44, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.083A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'K' and resid 29 through 30 Processing sheet with id=46, first strand: chain 'K' and resid 36 through 37 removed outlier: 7.204A pdb=" N VAL K 36 " --> pdb=" O LEU K 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=46 Processing sheet with id=47, first strand: chain 'K' and resid 48 through 55 removed outlier: 3.959A pdb=" N ASP K 286 " --> pdb=" O LYS K 277 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'K' and resid 227 through 229 removed outlier: 3.516A pdb=" N LEU K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR K 204 " --> pdb=" O VAL K 193 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL K 90 " --> pdb=" O PHE K 194 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'K' and resid 104 through 107 Processing sheet with id=50, first strand: chain 'K' and resid 118 through 121 removed outlier: 3.631A pdb=" N LEU K 118 " --> pdb=" O LYS K 129 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 129 " --> pdb=" O LEU K 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL K 120 " --> pdb=" O PHE K 127 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL K 126 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER K 172 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'K' and resid 133 through 135 removed outlier: 6.806A pdb=" N GLN K 134 " --> pdb=" O SER K 161 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'K' and resid 140 through 141 Processing sheet with id=53, first strand: chain 'K' and resid 310 through 318 removed outlier: 6.809A pdb=" N VAL K 593 " --> pdb=" O THR K 314 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN K 316 " --> pdb=" O GLY K 591 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY K 591 " --> pdb=" O ASN K 316 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY K 592 " --> pdb=" O GLN K 611 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 356 through 358 Processing sheet with id=55, first strand: chain 'K' and resid 377 through 378 removed outlier: 3.505A pdb=" N LYS K 377 " --> pdb=" O VAL K 432 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'K' and resid 451 through 453 Processing sheet with id=57, first strand: chain 'K' and resid 472 through 473 removed outlier: 3.943A pdb=" N TYR K 487 " --> pdb=" O TYR K 472 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'K' and resid 537 through 538 removed outlier: 3.620A pdb=" N ILE K 585 " --> pdb=" O ASP K 572 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP K 572 " --> pdb=" O ILE K 585 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY K 564 " --> pdb=" O ASP K 572 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'K' and resid 652 through 653 removed outlier: 6.405A pdb=" N GLU K 652 " --> pdb=" O ALA K 692 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N THR K 694 " --> pdb=" O GLU K 652 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'K' and resid 709 through 711 Processing sheet with id=61, first strand: chain 'K' and resid 715 through 726 removed outlier: 3.505A pdb=" N SER K 719 " --> pdb=" O THR K1064 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR K1065 " --> pdb=" O HIS K1046 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N HIS K1046 " --> pdb=" O TYR K1065 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'K' and resid 731 through 734 removed outlier: 4.655A pdb=" N LYS K 731 " --> pdb=" O LEU K 859 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'K' and resid 1118 through 1119 Processing sheet with id=64, first strand: chain 'K' and resid 1092 through 1095 Processing sheet with id=65, first strand: chain 'L' and resid 131 through 132 removed outlier: 3.657A pdb=" N VAL L 132 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU L 142 " --> pdb=" O VAL L 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=65 Processing sheet with id=66, first strand: chain 'L' and resid 347 through 352 removed outlier: 6.083A pdb=" N ASP L 355 " --> pdb=" O LEU L 351 " (cutoff:3.500A) 1668 hydrogen bonds defined for protein. 4707 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: 17.66 Time building geometry restraints manager: 11.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12545 1.34 - 1.46: 10050 1.46 - 1.58: 17971 1.58 - 1.71: 0 1.71 - 1.83: 285 Bond restraints: 40851 Sorted by residual: bond pdb=" C1 NAG L 701 " pdb=" O5 NAG L 701 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C1 NAG K1309 " pdb=" O5 NAG K1309 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 40846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 54496 1.88 - 3.77: 920 3.77 - 5.65: 122 5.65 - 7.54: 16 7.54 - 9.42: 3 Bond angle restraints: 55557 Sorted by residual: angle pdb=" C LEU K 982 " pdb=" N ASP K 983 " pdb=" CA ASP K 983 " ideal model delta sigma weight residual 120.94 130.36 -9.42 1.90e+00 2.77e-01 2.46e+01 angle pdb=" C LEU B 982 " pdb=" N ASP B 983 " pdb=" CA ASP B 983 " ideal model delta sigma weight residual 120.94 130.34 -9.40 1.90e+00 2.77e-01 2.45e+01 angle pdb=" C LEU A 982 " pdb=" N ASP A 983 " pdb=" CA ASP A 983 " ideal model delta sigma weight residual 120.94 130.33 -9.39 1.90e+00 2.77e-01 2.44e+01 angle pdb=" CA CYS K 736 " pdb=" CB CYS K 736 " pdb=" SG CYS K 736 " ideal model delta sigma weight residual 114.40 120.07 -5.67 2.30e+00 1.89e-01 6.09e+00 angle pdb=" CA CYS A 736 " pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " ideal model delta sigma weight residual 114.40 120.05 -5.65 2.30e+00 1.89e-01 6.04e+00 ... (remaining 55552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 23672 23.38 - 46.76: 1303 46.76 - 70.13: 198 70.13 - 93.51: 69 93.51 - 116.89: 33 Dihedral angle restraints: 25275 sinusoidal: 11040 harmonic: 14235 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 25.45 67.55 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS L 133 " pdb=" SG CYS L 133 " pdb=" SG CYS L 141 " pdb=" CB CYS L 141 " ideal model delta sinusoidal sigma weight residual 93.00 25.45 67.55 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 25.46 67.54 1 1.00e+01 1.00e-02 5.93e+01 ... (remaining 25272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 6183 0.111 - 0.222: 153 0.222 - 0.334: 6 0.334 - 0.445: 0 0.445 - 0.556: 3 Chirality restraints: 6345 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN L 103 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.70e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 103 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.69e+00 ... (remaining 6342 not shown) Planarity restraints: 7107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 904 " -0.015 2.00e-02 2.50e+03 1.59e-02 4.42e+00 pdb=" CG PHE K 904 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE K 904 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE K 904 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE K 904 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 904 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE K 904 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 904 " 0.015 2.00e-02 2.50e+03 1.59e-02 4.42e+00 pdb=" CG PHE A 904 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 904 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 904 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 904 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 904 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 904 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 904 " 0.015 2.00e-02 2.50e+03 1.58e-02 4.35e+00 pdb=" CG PHE B 904 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 904 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 904 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 904 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 904 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 904 " 0.001 2.00e-02 2.50e+03 ... (remaining 7104 not shown) Histogram of nonbonded interaction distances: 0.15 - 1.10: 27 1.10 - 2.05: 117 2.05 - 3.00: 22444 3.00 - 3.95: 104619 3.95 - 4.90: 192758 Warning: very small nonbonded interaction distances. Nonbonded interactions: 319965 Sorted by model distance: nonbonded pdb=" CG1 VAL A 42 " pdb=" NE ARG K 565 " model vdw 0.154 3.540 nonbonded pdb=" NE ARG A 565 " pdb=" CG1 VAL B 42 " model vdw 0.161 3.540 nonbonded pdb=" NE ARG B 565 " pdb=" CG1 VAL K 42 " model vdw 0.164 3.540 nonbonded pdb=" CE2 PHE B 590 " pdb=" NZ LYS K 852 " model vdw 0.401 3.420 nonbonded pdb=" CE2 PHE A 590 " pdb=" NZ LYS B 852 " model vdw 0.405 3.420 ... (remaining 319960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.300 Construct map_model_manager: 0.040 Extract box with map and model: 1.460 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 87.350 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 0.079 40851 Z= 0.289 Angle : 0.581 9.423 55557 Z= 0.286 Chirality : 0.046 0.556 6345 Planarity : 0.004 0.045 7050 Dihedral : 15.168 116.889 15969 Min Nonbonded Distance : 0.154 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4824 helix: 2.45 (0.13), residues: 1782 sheet: -0.98 (0.19), residues: 726 loop : -1.47 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 163 HIS 0.005 0.001 HIS K1062 PHE 0.037 0.001 PHE K 904 TYR 0.015 0.001 TYR K1065 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9022 (mt) cc_final: 0.8445 (mm) REVERT: A 867 MET cc_start: 0.8957 (mtt) cc_final: 0.8738 (mtt) REVERT: A 884 TRP cc_start: 0.8752 (p90) cc_final: 0.8121 (p90) REVERT: D 123 MET cc_start: -0.1449 (mtt) cc_final: -0.2085 (tmm) REVERT: D 152 MET cc_start: 0.2675 (mmt) cc_final: -0.1642 (pp-130) REVERT: D 332 MET cc_start: 0.2156 (ppp) cc_final: 0.1889 (ptm) REVERT: D 383 MET cc_start: 0.3343 (mtt) cc_final: 0.2781 (mtp) REVERT: B 738 MET cc_start: 0.8905 (tpt) cc_final: 0.8613 (tpt) REVERT: B 821 PHE cc_start: 0.8402 (t80) cc_final: 0.8152 (t80) REVERT: B 867 MET cc_start: 0.8930 (mtt) cc_final: 0.8678 (mtt) REVERT: C 123 MET cc_start: -0.0538 (mtt) cc_final: -0.1265 (tmm) REVERT: C 152 MET cc_start: 0.2936 (mmt) cc_final: -0.0802 (pp-130) REVERT: C 332 MET cc_start: 0.2117 (ppp) cc_final: 0.1865 (ptm) REVERT: C 383 MET cc_start: 0.2813 (mtt) cc_final: 0.2299 (mtp) REVERT: C 462 MET cc_start: 0.3742 (mpp) cc_final: 0.3451 (mpm) REVERT: K 821 PHE cc_start: 0.8457 (t80) cc_final: 0.7846 (t80) REVERT: L 123 MET cc_start: -0.1060 (mtt) cc_final: -0.1444 (pp-130) REVERT: L 152 MET cc_start: 0.3042 (mmt) cc_final: -0.0573 (pp-130) REVERT: L 332 MET cc_start: 0.2280 (ppp) cc_final: 0.2062 (ptm) REVERT: L 383 MET cc_start: 0.3563 (mtt) cc_final: 0.2989 (mtp) REVERT: L 462 MET cc_start: 0.3567 (mpp) cc_final: 0.3324 (mmm) outliers start: 0 outliers final: 1 residues processed: 417 average time/residue: 1.4543 time to fit residues: 744.5835 Evaluate side-chains 209 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 168 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 3.9990 chunk 366 optimal weight: 0.8980 chunk 203 optimal weight: 40.0000 chunk 125 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 378 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 chunk 230 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 438 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS D 194 ASN D 508 ASN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS B 753 GLN C 194 ASN C 508 ASN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS L 508 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 40851 Z= 0.364 Angle : 0.647 11.066 55557 Z= 0.335 Chirality : 0.046 0.225 6345 Planarity : 0.005 0.107 7050 Dihedral : 10.756 105.202 6902 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.92 % Allowed : 7.29 % Favored : 90.80 % 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: 0.10 (0.12), residues: 4824 helix: 2.36 (0.12), residues: 1791 sheet: -0.73 (0.19), residues: 693 loop : -1.61 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 477 HIS 0.011 0.001 HIS A 623 PHE 0.052 0.002 PHE A 560 TYR 0.024 0.002 TYR A 170 ARG 0.021 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7708 (tm130) REVERT: A 561 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6608 (mp10) REVERT: A 626 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7523 (mt0) REVERT: A 884 TRP cc_start: 0.8761 (p90) cc_final: 0.8141 (p90) REVERT: D 123 MET cc_start: -0.1354 (mtt) cc_final: -0.1792 (tmm) REVERT: D 332 MET cc_start: 0.2546 (ppp) cc_final: 0.2129 (ptm) REVERT: B 561 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: B 626 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7277 (mt0) REVERT: B 821 PHE cc_start: 0.8417 (t80) cc_final: 0.8167 (t80) REVERT: B 992 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: C 123 MET cc_start: -0.0537 (mtt) cc_final: -0.1259 (tmm) REVERT: C 152 MET cc_start: 0.2135 (mmt) cc_final: -0.0304 (pp-130) REVERT: C 297 MET cc_start: -0.0868 (mtt) cc_final: -0.1100 (mtm) REVERT: C 332 MET cc_start: 0.2391 (ppp) cc_final: 0.1976 (ptm) REVERT: C 480 MET cc_start: 0.1898 (ptt) cc_final: 0.1536 (ptt) REVERT: K 127 PHE cc_start: 0.7773 (m-80) cc_final: 0.7369 (t80) REVERT: K 270 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: K 561 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6458 (mp10) REVERT: K 626 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7251 (mt0) REVERT: K 821 PHE cc_start: 0.8425 (t80) cc_final: 0.7857 (t80) REVERT: L 152 MET cc_start: 0.2546 (mmt) cc_final: 0.0382 (pp-130) REVERT: L 297 MET cc_start: -0.0185 (mtt) cc_final: -0.0452 (mtm) REVERT: L 332 MET cc_start: 0.2383 (ppp) cc_final: 0.2054 (ptm) outliers start: 82 outliers final: 22 residues processed: 286 average time/residue: 1.3824 time to fit residues: 493.9358 Evaluate side-chains 216 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 4.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 527 LYS Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 527 LYS Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 561 GLN Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain K residue 958 ASN Chi-restraints excluded: chain L residue 555 PHE Chi-restraints excluded: chain L residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 365 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 439 optimal weight: 40.0000 chunk 474 optimal weight: 40.0000 chunk 391 optimal weight: 0.7980 chunk 435 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 623 HIS A 899 GLN D 373 HIS B 238 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 ASN B 623 HIS B 899 GLN C 373 HIS K 207 HIS ** K 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 604 ASN K 623 HIS L 194 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 40851 Z= 0.422 Angle : 0.656 9.711 55557 Z= 0.335 Chirality : 0.049 0.614 6345 Planarity : 0.005 0.059 7050 Dihedral : 9.458 95.060 6900 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.78 % Allowed : 10.65 % Favored : 87.57 % 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: -0.15 (0.12), residues: 4824 helix: 2.09 (0.12), residues: 1800 sheet: -0.98 (0.19), residues: 717 loop : -1.67 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 271 HIS 0.012 0.001 HIS A 623 PHE 0.022 0.002 PHE B1087 TYR 0.020 0.002 TYR B1065 ARG 0.008 0.001 ARG K1037 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 208 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7808 (tm130) REVERT: A 323 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8162 (pt0) REVERT: A 626 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7617 (mt0) REVERT: A 884 TRP cc_start: 0.8710 (p90) cc_final: 0.8111 (p90) REVERT: D 123 MET cc_start: -0.0834 (mtt) cc_final: -0.1854 (tmm) REVERT: D 332 MET cc_start: 0.2778 (ppp) cc_final: 0.2331 (ptm) REVERT: B 626 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7319 (mt0) REVERT: B 821 PHE cc_start: 0.8465 (t80) cc_final: 0.8241 (t80) REVERT: B 992 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: C 123 MET cc_start: -0.0239 (mtt) cc_final: -0.1241 (tmm) REVERT: C 278 LEU cc_start: -0.0872 (mt) cc_final: -0.1514 (tp) REVERT: C 332 MET cc_start: 0.2479 (ppp) cc_final: 0.2066 (ptm) REVERT: K 127 PHE cc_start: 0.7905 (m-80) cc_final: 0.7466 (t80) REVERT: K 270 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: K 313 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.7710 (tm130) REVERT: K 626 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7360 (mt0) REVERT: L 243 TYR cc_start: 0.0891 (OUTLIER) cc_final: 0.0410 (t80) REVERT: L 332 MET cc_start: 0.2502 (ppp) cc_final: 0.2158 (ptm) REVERT: L 579 MET cc_start: 0.6342 (mtt) cc_final: 0.5456 (mmm) outliers start: 76 outliers final: 35 residues processed: 262 average time/residue: 1.2521 time to fit residues: 417.8937 Evaluate side-chains 214 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 168 PHE Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain L residue 243 TYR Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 30.0000 chunk 330 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 209 optimal weight: 0.1980 chunk 295 optimal weight: 30.0000 chunk 440 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 chunk 417 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS A 899 GLN D 117 ASN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS B 899 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 40851 Z= 0.157 Angle : 0.556 10.716 55557 Z= 0.280 Chirality : 0.045 0.860 6345 Planarity : 0.004 0.042 7050 Dihedral : 8.224 81.212 6900 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.82 % Allowed : 11.56 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 4824 helix: 2.33 (0.12), residues: 1779 sheet: -0.57 (0.19), residues: 711 loop : -1.57 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 302 HIS 0.014 0.001 HIS A 623 PHE 0.036 0.001 PHE K 168 TYR 0.021 0.001 TYR C 587 ARG 0.003 0.000 ARG B 981 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 192 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.5260 (OUTLIER) cc_final: 0.5050 (p) REVERT: A 140 PHE cc_start: 0.7656 (p90) cc_final: 0.7414 (p90) REVERT: A 215 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 323 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: A 626 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7573 (mt0) REVERT: A 884 TRP cc_start: 0.8643 (p90) cc_final: 0.8030 (p90) REVERT: D 123 MET cc_start: -0.1192 (mtt) cc_final: -0.2011 (tmm) REVERT: D 243 TYR cc_start: 0.0642 (OUTLIER) cc_final: 0.0073 (t80) REVERT: D 332 MET cc_start: 0.2677 (ppp) cc_final: 0.2248 (ptm) REVERT: D 373 HIS cc_start: 0.2009 (OUTLIER) cc_final: 0.1763 (t-90) REVERT: B 131 CYS cc_start: 0.5287 (OUTLIER) cc_final: 0.5003 (p) REVERT: B 215 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 626 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7314 (mt0) REVERT: B 821 PHE cc_start: 0.8405 (t80) cc_final: 0.8128 (t80) REVERT: B 867 MET cc_start: 0.8848 (mtt) cc_final: 0.8558 (mtt) REVERT: C 123 MET cc_start: -0.0412 (mtt) cc_final: -0.1178 (tmm) REVERT: C 152 MET cc_start: 0.2955 (tpt) cc_final: 0.2738 (tpt) REVERT: C 243 TYR cc_start: 0.0944 (OUTLIER) cc_final: 0.0632 (t80) REVERT: C 270 MET cc_start: -0.1737 (pmm) cc_final: -0.2090 (mtm) REVERT: C 278 LEU cc_start: -0.1154 (mt) cc_final: -0.1510 (tp) REVERT: C 332 MET cc_start: 0.2457 (ppp) cc_final: 0.2039 (ptm) REVERT: K 140 PHE cc_start: 0.7465 (p90) cc_final: 0.7249 (p90) REVERT: K 270 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8169 (mt0) REVERT: K 626 GLN cc_start: 0.7723 (mm-40) cc_final: 0.7399 (mt0) REVERT: K 778 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7399 (mm-30) REVERT: L 243 TYR cc_start: 0.0997 (OUTLIER) cc_final: 0.0469 (t80) REVERT: L 270 MET cc_start: -0.2445 (pmm) cc_final: -0.2848 (mtm) REVERT: L 332 MET cc_start: 0.2645 (ppp) cc_final: 0.2292 (ptm) REVERT: L 579 MET cc_start: 0.6355 (mtt) cc_final: 0.5428 (mmm) outliers start: 78 outliers final: 17 residues processed: 247 average time/residue: 1.2967 time to fit residues: 406.8506 Evaluate side-chains 200 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 4.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 373 HIS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 243 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 2.9990 chunk 265 optimal weight: 50.0000 chunk 6 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 419 optimal weight: 0.4980 chunk 117 optimal weight: 40.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 40851 Z= 0.355 Angle : 0.619 11.537 55557 Z= 0.313 Chirality : 0.047 0.853 6345 Planarity : 0.004 0.042 7050 Dihedral : 7.539 59.715 6900 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.52 % Allowed : 11.89 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4824 helix: 2.14 (0.12), residues: 1794 sheet: -0.67 (0.19), residues: 711 loop : -1.67 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.011 0.001 HIS K 623 PHE 0.026 0.002 PHE D 512 TYR 0.020 0.001 TYR K1065 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 182 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.5532 (OUTLIER) cc_final: 0.5249 (p) REVERT: A 140 PHE cc_start: 0.7726 (p90) cc_final: 0.7495 (p90) REVERT: A 202 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7518 (mptt) REVERT: A 323 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: A 626 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7594 (mt0) REVERT: A 738 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (tpp) REVERT: A 884 TRP cc_start: 0.8664 (p90) cc_final: 0.8102 (p90) REVERT: D 123 MET cc_start: -0.1067 (mtt) cc_final: -0.2016 (tmm) REVERT: D 297 MET cc_start: 0.0194 (OUTLIER) cc_final: -0.0061 (mpt) REVERT: D 332 MET cc_start: 0.2647 (ppp) cc_final: 0.2224 (ptm) REVERT: D 408 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.3508 (mmt) REVERT: B 131 CYS cc_start: 0.5304 (OUTLIER) cc_final: 0.5062 (p) REVERT: B 237 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5579 (p90) REVERT: B 626 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7297 (mt0) REVERT: B 821 PHE cc_start: 0.8446 (t80) cc_final: 0.8189 (t80) REVERT: C 123 MET cc_start: -0.0282 (mtt) cc_final: -0.1248 (tmm) REVERT: C 243 TYR cc_start: 0.0889 (OUTLIER) cc_final: 0.0550 (t80) REVERT: C 270 MET cc_start: -0.1776 (pmm) cc_final: -0.2158 (mtm) REVERT: C 278 LEU cc_start: -0.1034 (mt) cc_final: -0.1362 (tp) REVERT: C 332 MET cc_start: 0.2426 (ppp) cc_final: 0.1991 (ptm) REVERT: K 140 PHE cc_start: 0.7535 (p90) cc_final: 0.7319 (p90) REVERT: K 270 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: K 313 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7723 (tm130) REVERT: K 626 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7433 (mt0) REVERT: L 332 MET cc_start: 0.2708 (ppp) cc_final: 0.2345 (ptm) REVERT: L 579 MET cc_start: 0.6317 (mtt) cc_final: 0.5414 (mmm) outliers start: 108 outliers final: 38 residues processed: 263 average time/residue: 1.2858 time to fit residues: 432.1990 Evaluate side-chains 218 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 738 MET Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 535 HIS Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 0.0170 chunk 420 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 274 optimal weight: 40.0000 chunk 115 optimal weight: 50.0000 chunk 467 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 245 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN D 373 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 373 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40851 Z= 0.177 Angle : 0.552 14.288 55557 Z= 0.279 Chirality : 0.045 0.771 6345 Planarity : 0.004 0.039 7050 Dihedral : 6.679 59.508 6900 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.13 % Allowed : 12.61 % Favored : 85.26 % 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: 0.14 (0.12), residues: 4824 helix: 2.35 (0.12), residues: 1764 sheet: -0.48 (0.19), residues: 711 loop : -1.58 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.012 0.001 HIS K 623 PHE 0.033 0.001 PHE L 464 TYR 0.022 0.001 TYR C 50 ARG 0.002 0.000 ARG B 981 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 183 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.5387 (OUTLIER) cc_final: 0.5139 (p) REVERT: A 140 PHE cc_start: 0.7736 (p90) cc_final: 0.7511 (p90) REVERT: A 202 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7538 (mptt) REVERT: A 323 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: A 626 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7622 (mt0) REVERT: A 884 TRP cc_start: 0.8613 (p90) cc_final: 0.8046 (p90) REVERT: D 123 MET cc_start: -0.1097 (mtt) cc_final: -0.1951 (pp-130) REVERT: D 243 TYR cc_start: 0.0577 (OUTLIER) cc_final: 0.0037 (t80) REVERT: D 332 MET cc_start: 0.2720 (ppp) cc_final: 0.2345 (ptm) REVERT: B 131 CYS cc_start: 0.5339 (OUTLIER) cc_final: 0.5057 (p) REVERT: B 202 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7632 (mmtm) REVERT: B 237 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.5529 (p90) REVERT: B 325 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6907 (tt) REVERT: B 626 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7368 (mt0) REVERT: B 738 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8529 (ttt) REVERT: B 821 PHE cc_start: 0.8406 (t80) cc_final: 0.8167 (t80) REVERT: B 900 MET cc_start: 0.8946 (mmt) cc_final: 0.8658 (mmp) REVERT: C 123 MET cc_start: -0.0391 (mtt) cc_final: -0.1280 (tmm) REVERT: C 243 TYR cc_start: 0.0843 (OUTLIER) cc_final: 0.0488 (t80) REVERT: C 278 LEU cc_start: -0.1031 (mt) cc_final: -0.1381 (tp) REVERT: C 332 MET cc_start: 0.2221 (ppp) cc_final: 0.1858 (ptm) REVERT: K 140 PHE cc_start: 0.7520 (p90) cc_final: 0.7310 (p90) REVERT: K 202 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7663 (mptt) REVERT: K 270 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: K 323 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: K 626 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7466 (mt0) REVERT: K 778 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7475 (mm-30) REVERT: L 270 MET cc_start: -0.2125 (pmm) cc_final: -0.2630 (mtm) REVERT: L 332 MET cc_start: 0.2678 (ppp) cc_final: 0.2282 (ptm) outliers start: 91 outliers final: 27 residues processed: 252 average time/residue: 1.3558 time to fit residues: 434.7821 Evaluate side-chains 215 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 323 GLU Chi-restraints excluded: chain K residue 325 ILE Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 535 HIS Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 30.0000 chunk 341 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 393 optimal weight: 0.0870 chunk 260 optimal weight: 3.9990 chunk 465 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 283 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 40851 Z= 0.369 Angle : 0.628 14.780 55557 Z= 0.319 Chirality : 0.047 0.749 6345 Planarity : 0.005 0.047 7050 Dihedral : 6.724 58.789 6900 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.08 % Allowed : 13.57 % Favored : 84.35 % 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: -0.03 (0.12), residues: 4824 helix: 2.16 (0.12), residues: 1770 sheet: -0.59 (0.19), residues: 696 loop : -1.64 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 349 HIS 0.010 0.001 HIS K 623 PHE 0.036 0.002 PHE D 512 TYR 0.020 0.001 TYR K1065 ARG 0.004 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 181 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 CYS cc_start: 0.5652 (OUTLIER) cc_final: 0.5384 (p) REVERT: A 140 PHE cc_start: 0.7721 (p90) cc_final: 0.7518 (p90) REVERT: A 202 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7340 (mptt) REVERT: A 215 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7848 (t80) REVERT: A 323 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: A 626 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7560 (mt0) REVERT: A 738 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8425 (ttt) REVERT: A 884 TRP cc_start: 0.8625 (p90) cc_final: 0.8074 (p90) REVERT: D 123 MET cc_start: -0.0959 (mtt) cc_final: -0.1998 (tmm) REVERT: D 243 TYR cc_start: 0.0494 (OUTLIER) cc_final: -0.0034 (t80) REVERT: D 332 MET cc_start: 0.2539 (ppp) cc_final: 0.2127 (ptm) REVERT: B 131 CYS cc_start: 0.5440 (OUTLIER) cc_final: 0.5232 (p) REVERT: B 202 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7556 (mmtm) REVERT: B 237 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.5506 (p90) REVERT: B 325 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7032 (tt) REVERT: B 626 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7400 (mt0) REVERT: B 738 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8527 (ttt) REVERT: B 821 PHE cc_start: 0.8455 (t80) cc_final: 0.8225 (t80) REVERT: B 992 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: C 123 MET cc_start: -0.0254 (mtt) cc_final: -0.1107 (tmm) REVERT: C 243 TYR cc_start: 0.0820 (OUTLIER) cc_final: 0.0450 (t80) REVERT: C 270 MET cc_start: -0.1594 (pmm) cc_final: -0.2219 (mtm) REVERT: C 278 LEU cc_start: -0.1086 (mt) cc_final: -0.1437 (tp) REVERT: C 332 MET cc_start: 0.2211 (ppp) cc_final: 0.1864 (ptm) REVERT: K 140 PHE cc_start: 0.7626 (p90) cc_final: 0.7419 (p90) REVERT: K 202 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7554 (mptt) REVERT: K 270 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: K 313 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7723 (tm130) REVERT: K 626 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7431 (mt0) REVERT: K 884 TRP cc_start: 0.8612 (p90) cc_final: 0.8178 (p90) REVERT: L 297 MET cc_start: 0.0324 (OUTLIER) cc_final: 0.0081 (mpp) REVERT: L 332 MET cc_start: 0.2616 (ppp) cc_final: 0.2182 (ptm) outliers start: 89 outliers final: 40 residues processed: 249 average time/residue: 1.2691 time to fit residues: 402.7157 Evaluate side-chains 229 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 325 ILE Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 738 MET Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 535 HIS Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 30.0000 chunk 185 optimal weight: 0.8980 chunk 278 optimal weight: 7.9990 chunk 140 optimal weight: 50.0000 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 295 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 overall best weight: 2.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40851 Z= 0.271 Angle : 0.590 14.371 55557 Z= 0.298 Chirality : 0.046 0.730 6345 Planarity : 0.004 0.042 7050 Dihedral : 6.591 59.939 6900 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.06 % Allowed : 14.04 % Favored : 83.91 % 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: 0.01 (0.12), residues: 4824 helix: 2.17 (0.12), residues: 1773 sheet: -0.54 (0.19), residues: 696 loop : -1.60 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 302 HIS 0.010 0.001 HIS K 623 PHE 0.048 0.002 PHE D 512 TYR 0.016 0.001 TYR K1065 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 176 time to evaluate : 4.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7728 (p90) cc_final: 0.7517 (p90) REVERT: A 202 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7603 (mptt) REVERT: A 205 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8528 (t) REVERT: A 215 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7840 (t80) REVERT: A 323 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: A 626 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7564 (mt0) REVERT: A 738 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8657 (tpp) REVERT: A 884 TRP cc_start: 0.8600 (p90) cc_final: 0.8060 (p90) REVERT: D 123 MET cc_start: -0.0963 (mtt) cc_final: -0.1887 (pp-130) REVERT: D 243 TYR cc_start: 0.0506 (OUTLIER) cc_final: -0.0029 (t80) REVERT: D 332 MET cc_start: 0.2502 (ppp) cc_final: 0.2065 (ptm) REVERT: B 202 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7595 (mmtm) REVERT: B 237 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5309 (p90) REVERT: B 325 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6898 (tt) REVERT: B 626 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7440 (mt0) REVERT: B 738 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8520 (ttt) REVERT: B 821 PHE cc_start: 0.8440 (t80) cc_final: 0.8210 (t80) REVERT: B 898 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8325 (mtt) REVERT: C 123 MET cc_start: -0.0289 (mtt) cc_final: -0.0936 (tmm) REVERT: C 243 TYR cc_start: 0.0802 (OUTLIER) cc_final: 0.0427 (t80) REVERT: C 270 MET cc_start: -0.1542 (pmm) cc_final: -0.2212 (mtm) REVERT: C 278 LEU cc_start: -0.1005 (mt) cc_final: -0.1367 (tp) REVERT: C 332 MET cc_start: 0.2230 (ppp) cc_final: 0.1888 (ptm) REVERT: K 202 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7572 (mptt) REVERT: K 270 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: K 313 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7716 (tm130) REVERT: K 626 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7396 (mt0) REVERT: K 884 TRP cc_start: 0.8471 (p90) cc_final: 0.8093 (p90) REVERT: L 270 MET cc_start: -0.1926 (pmm) cc_final: -0.2330 (mtm) REVERT: L 297 MET cc_start: 0.0319 (OUTLIER) cc_final: 0.0086 (mpp) REVERT: L 332 MET cc_start: 0.2596 (ppp) cc_final: 0.2158 (ptm) outliers start: 88 outliers final: 37 residues processed: 242 average time/residue: 1.3153 time to fit residues: 405.3307 Evaluate side-chains 225 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 215 PHE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 535 HIS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 325 ILE Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 738 MET Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 3.9990 chunk 445 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 chunk 433 optimal weight: 30.0000 chunk 261 optimal weight: 0.8980 chunk 188 optimal weight: 40.0000 chunk 340 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 392 optimal weight: 7.9990 chunk 410 optimal weight: 1.9990 chunk 432 optimal weight: 30.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 40851 Z= 0.341 Angle : 0.626 14.623 55557 Z= 0.315 Chirality : 0.047 0.715 6345 Planarity : 0.004 0.044 7050 Dihedral : 6.608 59.931 6900 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.92 % Allowed : 14.44 % Favored : 83.65 % 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: -0.08 (0.12), residues: 4824 helix: 2.04 (0.12), residues: 1788 sheet: -0.82 (0.19), residues: 729 loop : -1.55 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 302 HIS 0.009 0.001 HIS L 535 PHE 0.055 0.002 PHE D 512 TYR 0.018 0.001 TYR K1065 ARG 0.005 0.000 ARG K1037 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 176 time to evaluate : 4.099 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7730 (p90) cc_final: 0.7519 (p90) REVERT: A 202 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7463 (mptt) REVERT: A 205 SER cc_start: 0.8746 (OUTLIER) cc_final: 0.8519 (t) REVERT: A 323 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8019 (pt0) REVERT: A 626 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7583 (mt0) REVERT: A 884 TRP cc_start: 0.8575 (p90) cc_final: 0.8051 (p90) REVERT: D 123 MET cc_start: -0.0889 (mtt) cc_final: -0.1807 (pp-130) REVERT: D 243 TYR cc_start: 0.0562 (OUTLIER) cc_final: 0.0062 (t80) REVERT: D 332 MET cc_start: 0.2811 (ppp) cc_final: 0.2390 (ptm) REVERT: D 408 MET cc_start: 0.2901 (pmm) cc_final: 0.2582 (ptp) REVERT: B 202 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7593 (mptt) REVERT: B 237 PHE cc_start: 0.5987 (OUTLIER) cc_final: 0.5124 (p90) REVERT: B 325 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6931 (tt) REVERT: B 626 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7432 (mt0) REVERT: B 738 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8499 (ttt) REVERT: B 821 PHE cc_start: 0.8453 (t80) cc_final: 0.8215 (t80) REVERT: B 898 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8391 (mtt) REVERT: B 992 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: C 243 TYR cc_start: 0.0804 (OUTLIER) cc_final: 0.0422 (t80) REVERT: C 270 MET cc_start: -0.1323 (pmm) cc_final: -0.1956 (mtt) REVERT: C 278 LEU cc_start: -0.0921 (mt) cc_final: -0.1301 (tp) REVERT: C 332 MET cc_start: 0.2376 (ppp) cc_final: 0.2036 (ptm) REVERT: K 202 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7595 (mptt) REVERT: K 270 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: K 313 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7724 (tm130) REVERT: K 626 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7394 (mt0) REVERT: K 884 TRP cc_start: 0.8566 (p90) cc_final: 0.8107 (p90) REVERT: L 297 MET cc_start: 0.0348 (OUTLIER) cc_final: 0.0121 (mpp) REVERT: L 332 MET cc_start: 0.2448 (ppp) cc_final: 0.2007 (ptm) REVERT: L 557 MET cc_start: 0.0142 (ppp) cc_final: -0.0146 (ppp) outliers start: 82 outliers final: 36 residues processed: 237 average time/residue: 1.3102 time to fit residues: 393.9951 Evaluate side-chains 224 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 325 ILE Chi-restraints excluded: chain K residue 547 THR Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 738 MET Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 297 MET Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 40.0000 chunk 458 optimal weight: 8.9990 chunk 279 optimal weight: 40.0000 chunk 217 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 481 optimal weight: 0.9980 chunk 442 optimal weight: 20.0000 chunk 383 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 295 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 40851 Z= 0.381 Angle : 0.647 14.270 55557 Z= 0.326 Chirality : 0.048 0.704 6345 Planarity : 0.005 0.050 7050 Dihedral : 6.645 59.996 6900 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.57 % Allowed : 14.81 % Favored : 83.63 % 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: -0.15 (0.12), residues: 4824 helix: 1.96 (0.12), residues: 1788 sheet: -0.64 (0.19), residues: 699 loop : -1.66 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 302 HIS 0.010 0.001 HIS C 535 PHE 0.054 0.002 PHE D 512 TYR 0.019 0.001 TYR K1065 ARG 0.005 0.001 ARG D 582 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 4.313 Fit side-chains revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7731 (p90) cc_final: 0.7519 (p90) REVERT: A 202 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7459 (mptt) REVERT: A 205 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8557 (t) REVERT: A 323 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8013 (pt0) REVERT: A 626 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7582 (mt0) REVERT: A 884 TRP cc_start: 0.8578 (p90) cc_final: 0.8065 (p90) REVERT: D 123 MET cc_start: -0.0812 (mtt) cc_final: -0.1766 (pp-130) REVERT: D 243 TYR cc_start: 0.0586 (OUTLIER) cc_final: 0.0106 (t80) REVERT: D 332 MET cc_start: 0.2833 (ppp) cc_final: 0.2417 (ptm) REVERT: D 462 MET cc_start: 0.1305 (ptp) cc_final: 0.1096 (mmp) REVERT: B 202 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7577 (mptt) REVERT: B 237 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5035 (p90) REVERT: B 325 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6917 (tt) REVERT: B 626 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7445 (mt0) REVERT: B 738 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8513 (ttt) REVERT: B 821 PHE cc_start: 0.8461 (t80) cc_final: 0.8246 (t80) REVERT: B 898 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8411 (mtt) REVERT: B 992 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: C 123 MET cc_start: 0.0234 (mtm) cc_final: -0.1698 (tmm) REVERT: C 243 TYR cc_start: 0.0812 (OUTLIER) cc_final: 0.0422 (t80) REVERT: C 270 MET cc_start: -0.1386 (pmm) cc_final: -0.2005 (mtt) REVERT: C 278 LEU cc_start: -0.0950 (mt) cc_final: -0.1315 (tp) REVERT: C 332 MET cc_start: 0.2513 (ppp) cc_final: 0.2180 (ptm) REVERT: K 202 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: K 313 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7732 (tm130) REVERT: K 626 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7422 (mt0) REVERT: K 884 TRP cc_start: 0.8583 (p90) cc_final: 0.8150 (p90) REVERT: L 270 MET cc_start: -0.1824 (pmm) cc_final: -0.2383 (mtm) REVERT: L 297 MET cc_start: 0.0293 (OUTLIER) cc_final: 0.0076 (mpp) REVERT: L 332 MET cc_start: 0.2449 (ppp) cc_final: 0.2005 (ptm) outliers start: 67 outliers final: 35 residues processed: 228 average time/residue: 1.3410 time to fit residues: 390.2228 Evaluate side-chains 222 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 937 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 992 ASP Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 205 SER Chi-restraints excluded: chain K residue 237 PHE Chi-restraints excluded: chain K residue 313 GLN Chi-restraints excluded: chain K residue 325 ILE Chi-restraints excluded: chain K residue 547 THR Chi-restraints excluded: chain K residue 551 THR Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 738 MET Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain K residue 900 MET Chi-restraints excluded: chain K residue 937 PHE Chi-restraints excluded: chain L residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 353 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 394 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 HIS ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.199296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.128617 restraints weight = 90440.311| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 7.37 r_work: 0.3234 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 40851 Z= 0.401 Angle : 0.662 13.703 55557 Z= 0.333 Chirality : 0.048 0.686 6345 Planarity : 0.005 0.061 7050 Dihedral : 6.714 59.917 6900 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.47 % Allowed : 15.04 % Favored : 83.49 % 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: -0.23 (0.12), residues: 4824 helix: 1.89 (0.12), residues: 1785 sheet: -0.91 (0.19), residues: 729 loop : -1.61 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 302 HIS 0.023 0.001 HIS L 540 PHE 0.052 0.002 PHE D 512 TYR 0.020 0.001 TYR K1065 ARG 0.007 0.001 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11499.36 seconds wall clock time: 248 minutes 17.33 seconds (14897.33 seconds total)