Starting phenix.real_space_refine on Thu Jan 16 02:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_38690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_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/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_38690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_38690.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_38690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvm_38690/01_2025/8xvm_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 16.65, per 1000 atoms: 0.42 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=15, 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 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.5 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: 3.87 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: 13.28 Time building geometry restraints manager: 9.51 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: 0.80 - 1.62: 36 1.62 - 2.44: 292 2.44 - 3.26: 41166 3.26 - 4.08: 98935 4.08 - 4.90: 179467 Warning: very small nonbonded interaction distances. Nonbonded interactions: 319896 Sorted by model distance: nonbonded pdb=" NZ LYS A 41 " pdb=" CA GLN K 561 " model vdw 0.802 2.840 nonbonded pdb=" CA GLN A 561 " pdb=" NZ LYS B 41 " model vdw 0.804 2.840 nonbonded pdb=" CA GLN B 561 " pdb=" NZ LYS K 41 " model vdw 0.807 2.840 nonbonded pdb=" CE LYS A 852 " pdb=" CZ PHE K 590 " model vdw 0.858 2.992 nonbonded pdb=" CZ PHE B 590 " pdb=" CE LYS K 852 " model vdw 0.858 2.992 ... (remaining 319891 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: 0.19 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.050 Extract box with map and model: 1.180 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 66.770 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.980 ------------------------------------------------------------------------------- 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= 0.288 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 : 0.802 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 : 3.216 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: 1.1905 time to fit residues: 606.8103 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 : 3.191 ------------------------------------------------------------------------------- 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: 3.9990 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: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS D 194 ASN B 238 GLN ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 604 ASN B 623 HIS B 753 GLN C 194 ASN K 238 GLN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 GLN K 604 ASN K 623 HIS L 194 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.200526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.125750 restraints weight = 92097.769| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.99 r_work: 0.3225 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 40851 Z= 0.348 Angle : 0.651 23.146 55557 Z= 0.333 Chirality : 0.047 0.215 6345 Planarity : 0.005 0.094 7050 Dihedral : 10.177 101.064 6902 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.90 % Favored : 93.08 % Rotamer: Outliers : 1.85 % Allowed : 7.59 % Favored : 90.56 % 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: 2.32 (0.12), residues: 1788 sheet: -0.77 (0.19), residues: 711 loop : -1.66 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 477 HIS 0.011 0.001 HIS A 623 PHE 0.034 0.002 PHE A 560 TYR 0.026 0.002 TYR A 170 ARG 0.024 0.001 ARG K 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 305 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 226 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7016 (tp) REVERT: A 626 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7656 (mt0) REVERT: A 884 TRP cc_start: 0.8888 (p90) cc_final: 0.8327 (p90) REVERT: D 90 ASN cc_start: 0.0541 (OUTLIER) cc_final: 0.0063 (t0) REVERT: D 174 LYS cc_start: 0.5648 (mttt) cc_final: 0.5324 (tmmt) REVERT: D 227 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.4272 (mt-10) REVERT: D 332 MET cc_start: 0.2495 (ppp) cc_final: 0.1840 (ptm) REVERT: D 383 MET cc_start: 0.1542 (mtt) cc_final: 0.1239 (mtp) REVERT: D 504 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.5341 (t80) REVERT: B 171 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9045 (m) REVERT: B 313 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8569 (tp40) REVERT: B 626 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7422 (mt0) REVERT: C 90 ASN cc_start: 0.0309 (OUTLIER) cc_final: -0.0170 (t0) REVERT: C 115 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7653 (mtp180) REVERT: C 174 LYS cc_start: 0.5828 (mttt) cc_final: 0.5540 (tmmt) REVERT: C 332 MET cc_start: 0.2274 (ppp) cc_final: 0.1562 (ptm) REVERT: C 383 MET cc_start: 0.1607 (mtt) cc_final: 0.1374 (mtp) REVERT: C 504 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5560 (t80) REVERT: C 579 MET cc_start: 0.1812 (mtt) cc_final: -0.0947 (mmm) REVERT: K 127 PHE cc_start: 0.7980 (m-80) cc_final: 0.7619 (t80) REVERT: K 225 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6914 (tp) REVERT: K 270 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: K 626 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7338 (mt0) REVERT: K 821 PHE cc_start: 0.8799 (t80) cc_final: 0.8350 (t80) REVERT: L 90 ASN cc_start: 0.1011 (OUTLIER) cc_final: 0.0511 (t0) REVERT: L 174 LYS cc_start: 0.5637 (mttt) cc_final: 0.5312 (tmmt) REVERT: L 332 MET cc_start: 0.2368 (ppp) cc_final: 0.1813 (ptm) REVERT: L 383 MET cc_start: 0.1636 (mtt) cc_final: 0.1415 (mtp) REVERT: L 462 MET cc_start: 0.3709 (mpp) cc_final: 0.3389 (mpm) REVERT: L 504 PHE cc_start: 0.6158 (OUTLIER) cc_final: 0.5595 (t80) REVERT: L 579 MET cc_start: 0.2347 (mtt) cc_final: -0.0161 (mmm) outliers start: 79 outliers final: 21 residues processed: 279 average time/residue: 1.1112 time to fit residues: 387.3495 Evaluate side-chains 218 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 3.240 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 313 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 C residue 90 ASN Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 593 THR 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 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 K residue 958 ASN Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 504 PHE Chi-restraints excluded: chain L residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 379 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 237 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 347 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 292 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 604 ASN A 623 HIS ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS L 508 ASN ** L 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.208098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.137729 restraints weight = 89302.627| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 6.68 r_work: 0.3338 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 40851 Z= 0.170 Angle : 0.564 12.995 55557 Z= 0.285 Chirality : 0.043 0.231 6345 Planarity : 0.004 0.061 7050 Dihedral : 8.957 93.290 6900 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.49 % Allowed : 10.04 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.12), residues: 4824 helix: 2.39 (0.12), residues: 1788 sheet: -0.57 (0.19), residues: 714 loop : -1.55 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 271 HIS 0.013 0.001 HIS K 207 PHE 0.032 0.001 PHE A 168 TYR 0.020 0.001 TYR B 28 ARG 0.021 0.000 ARG A 565 *********************** 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 281 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 217 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7823 (p90) cc_final: 0.7610 (p90) REVERT: A 225 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6897 (tp) REVERT: A 323 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: A 626 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7691 (mt0) REVERT: D 82 MET cc_start: 0.3724 (ppp) cc_final: 0.3505 (ptm) REVERT: D 174 LYS cc_start: 0.5139 (mttt) cc_final: 0.4892 (tmmt) REVERT: D 227 GLU cc_start: 0.4728 (OUTLIER) cc_final: 0.3383 (mt-10) REVERT: D 243 TYR cc_start: -0.0299 (OUTLIER) cc_final: -0.1125 (t80) REVERT: D 332 MET cc_start: 0.2564 (ppp) cc_final: 0.1804 (ptm) REVERT: D 383 MET cc_start: 0.1481 (mtt) cc_final: 0.1204 (mtt) REVERT: D 504 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.4948 (t80) REVERT: B 626 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7457 (mt0) REVERT: B 867 MET cc_start: 0.9218 (mtt) cc_final: 0.8950 (mtt) REVERT: B 900 MET cc_start: 0.9103 (mmt) cc_final: 0.8855 (mmp) REVERT: C 115 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7563 (mtp180) REVERT: C 174 LYS cc_start: 0.5594 (mttt) cc_final: 0.5327 (tmmt) REVERT: C 332 MET cc_start: 0.2462 (ppp) cc_final: 0.1700 (ptm) REVERT: C 366 MET cc_start: -0.3756 (tpt) cc_final: -0.3979 (tpt) REVERT: C 383 MET cc_start: 0.1569 (mtt) cc_final: 0.1276 (mtp) REVERT: C 504 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5338 (t80) REVERT: C 579 MET cc_start: 0.0260 (mtt) cc_final: -0.1867 (mmm) REVERT: K 140 PHE cc_start: 0.7549 (p90) cc_final: 0.7327 (p90) REVERT: K 225 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6891 (tp) REVERT: K 270 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: K 626 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7424 (mt0) REVERT: K 778 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8397 (mm-30) REVERT: K 821 PHE cc_start: 0.8740 (t80) cc_final: 0.8257 (t80) REVERT: L 174 LYS cc_start: 0.5372 (mttt) cc_final: 0.5078 (tmmt) REVERT: L 235 PRO cc_start: 0.0121 (Cg_exo) cc_final: -0.0095 (Cg_endo) REVERT: L 243 TYR cc_start: 0.0238 (OUTLIER) cc_final: -0.0656 (t80) REVERT: L 270 MET cc_start: 0.2084 (OUTLIER) cc_final: 0.1813 (pmm) REVERT: L 332 MET cc_start: 0.2613 (ppp) cc_final: 0.1934 (ptm) REVERT: L 383 MET cc_start: 0.1460 (mtt) cc_final: 0.1209 (mtt) REVERT: L 462 MET cc_start: 0.4145 (mpp) cc_final: 0.3836 (mpm) REVERT: L 504 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5067 (t80) REVERT: L 579 MET cc_start: 0.0361 (mtt) cc_final: -0.1475 (mmm) outliers start: 64 outliers final: 14 residues processed: 264 average time/residue: 1.1080 time to fit residues: 365.2899 Evaluate side-chains 207 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain K residue 99 ASN Chi-restraints excluded: chain K residue 168 PHE 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 703 VAL Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain L residue 243 TYR Chi-restraints excluded: chain L residue 270 MET Chi-restraints excluded: chain L residue 504 PHE 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 319 optimal weight: 7.9990 chunk 246 optimal weight: 0.4980 chunk 119 optimal weight: 30.0000 chunk 364 optimal weight: 40.0000 chunk 115 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 313 optimal weight: 30.0000 chunk 390 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** D 373 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 HIS C 373 HIS ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS L 556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.207994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.133684 restraints weight = 85113.503| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 4.95 r_work: 0.3205 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 40851 Z= 0.322 Angle : 0.654 37.359 55557 Z= 0.321 Chirality : 0.049 0.844 6345 Planarity : 0.005 0.048 7050 Dihedral : 8.565 82.003 6900 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 2.08 % Allowed : 10.98 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.12), residues: 4824 helix: 2.25 (0.12), residues: 1788 sheet: -0.61 (0.19), residues: 735 loop : -1.62 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 271 HIS 0.012 0.001 HIS K 623 PHE 0.036 0.002 PHE C 464 TYR 0.019 0.001 TYR K1065 ARG 0.012 0.001 ARG A 565 *********************** 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 287 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 198 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7133 (tp) REVERT: A 323 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: A 560 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7005 (p90) REVERT: A 626 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7721 (mt0) REVERT: A 884 TRP cc_start: 0.8881 (p90) cc_final: 0.8361 (p90) REVERT: D 174 LYS cc_start: 0.5552 (mttt) cc_final: 0.5236 (tmmt) REVERT: D 227 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.4209 (mt-10) REVERT: D 243 TYR cc_start: -0.0636 (OUTLIER) cc_final: -0.1344 (t80) REVERT: D 270 MET cc_start: 0.1472 (pmm) cc_final: 0.0774 (pmm) REVERT: D 332 MET cc_start: 0.2731 (ppp) cc_final: 0.2010 (ptm) REVERT: D 504 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5265 (t80) REVERT: B 626 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7466 (mt0) REVERT: B 738 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9222 (tpp) REVERT: C 115 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7732 (ttp-170) REVERT: C 332 MET cc_start: 0.2463 (ppp) cc_final: 0.1708 (ptm) REVERT: C 504 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5435 (t80) REVERT: C 579 MET cc_start: 0.1990 (mtt) cc_final: -0.0760 (mmm) REVERT: K 270 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: K 313 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8485 (tm130) REVERT: K 626 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7500 (mt0) REVERT: K 778 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8579 (mm-30) REVERT: K 821 PHE cc_start: 0.8769 (t80) cc_final: 0.8315 (t80) REVERT: L 62 MET cc_start: 0.1816 (mtm) cc_final: 0.1607 (mpp) REVERT: L 174 LYS cc_start: 0.5838 (mttt) cc_final: 0.5593 (tmmt) REVERT: L 243 TYR cc_start: -0.0139 (OUTLIER) cc_final: -0.0883 (t80) REVERT: L 332 MET cc_start: 0.2649 (ppp) cc_final: 0.2033 (ptm) REVERT: L 383 MET cc_start: 0.1499 (mtt) cc_final: 0.1037 (mtp) REVERT: L 408 MET cc_start: 0.5133 (mtt) cc_final: 0.4796 (mmt) REVERT: L 462 MET cc_start: 0.3912 (mpp) cc_final: 0.3659 (mpm) REVERT: L 579 MET cc_start: 0.1505 (mtt) cc_final: -0.1070 (mmm) outliers start: 89 outliers final: 27 residues processed: 263 average time/residue: 1.0955 time to fit residues: 360.8732 Evaluate side-chains 215 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 560 PHE 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 999 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 504 PHE Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain K residue 167 THR 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 L residue 90 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 220 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 443 optimal weight: 0.0470 chunk 134 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 391 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 423 optimal weight: 0.5980 chunk 481 optimal weight: 20.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 562 GLN K 623 HIS L 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.212113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138369 restraints weight = 86297.089| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 4.96 r_work: 0.3360 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 40851 Z= 0.170 Angle : 0.597 30.350 55557 Z= 0.290 Chirality : 0.047 0.838 6345 Planarity : 0.004 0.044 7050 Dihedral : 7.660 59.670 6900 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 1.96 % Allowed : 11.75 % Favored : 86.29 % 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: 0.26 (0.12), residues: 4824 helix: 2.41 (0.12), residues: 1779 sheet: -0.37 (0.19), residues: 729 loop : -1.53 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 271 HIS 0.012 0.001 HIS K 623 PHE 0.041 0.001 PHE B 560 TYR 0.015 0.001 TYR C 587 ARG 0.007 0.000 ARG K 565 *********************** 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 291 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7727 (p90) cc_final: 0.7486 (p90) REVERT: A 225 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6856 (tp) REVERT: A 323 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8170 (pt0) REVERT: A 626 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7690 (mt0) REVERT: D 174 LYS cc_start: 0.5167 (mttt) cc_final: 0.4877 (tmmt) REVERT: D 227 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.3635 (mt-10) REVERT: D 243 TYR cc_start: -0.0389 (OUTLIER) cc_final: -0.1138 (t80) REVERT: D 270 MET cc_start: 0.0809 (pmm) cc_final: 0.0133 (pmm) REVERT: D 332 MET cc_start: 0.2145 (ppp) cc_final: 0.1436 (ptm) REVERT: D 504 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5063 (t80) REVERT: B 215 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7433 (t80) REVERT: B 626 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7405 (mt0) REVERT: B 867 MET cc_start: 0.9183 (mtt) cc_final: 0.8927 (mtt) REVERT: C 115 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7652 (mtp180) REVERT: C 243 TYR cc_start: 0.0329 (OUTLIER) cc_final: -0.0300 (t80) REVERT: C 332 MET cc_start: 0.2327 (ppp) cc_final: 0.1489 (ptm) REVERT: C 504 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5209 (t80) REVERT: C 523 PHE cc_start: 0.3745 (m-80) cc_final: 0.3506 (m-10) REVERT: C 579 MET cc_start: 0.0733 (mtt) cc_final: -0.1362 (mmm) REVERT: K 140 PHE cc_start: 0.7470 (p90) cc_final: 0.7247 (p90) REVERT: K 270 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: K 626 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7494 (mt0) REVERT: K 778 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8319 (mm-30) REVERT: K 821 PHE cc_start: 0.8671 (t80) cc_final: 0.8173 (t80) REVERT: L 270 MET cc_start: 0.0562 (pmm) cc_final: 0.0284 (pmm) REVERT: L 332 MET cc_start: 0.2492 (ppp) cc_final: 0.1761 (ptm) REVERT: L 383 MET cc_start: 0.1558 (mtt) cc_final: 0.1333 (mtt) REVERT: L 408 MET cc_start: 0.4944 (OUTLIER) cc_final: 0.4528 (mmt) REVERT: L 462 MET cc_start: 0.4016 (mpp) cc_final: 0.3629 (mpm) REVERT: L 579 MET cc_start: 0.0614 (mtt) cc_final: -0.1529 (mmm) outliers start: 84 outliers final: 23 residues processed: 269 average time/residue: 1.1101 time to fit residues: 373.1847 Evaluate side-chains 213 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 535 HIS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 504 PHE 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 225 LEU Chi-restraints excluded: chain K residue 270 GLN Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 408 MET 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 65 optimal weight: 0.9990 chunk 431 optimal weight: 40.0000 chunk 389 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 199 optimal weight: 50.0000 chunk 306 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS ** B 196 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 221 GLN ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 623 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.211151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.138706 restraints weight = 87709.533| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 5.68 r_work: 0.3335 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 40851 Z= 0.217 Angle : 0.654 41.623 55557 Z= 0.312 Chirality : 0.046 0.775 6345 Planarity : 0.004 0.044 7050 Dihedral : 6.923 59.887 6900 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 1.99 % Allowed : 12.33 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4824 helix: 2.44 (0.12), residues: 1776 sheet: -0.43 (0.19), residues: 741 loop : -1.54 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 271 HIS 0.011 0.001 HIS K 623 PHE 0.046 0.001 PHE B 560 TYR 0.020 0.001 TYR A 170 ARG 0.008 0.000 ARG A 190 *********************** 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 278 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 193 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7798 (p90) cc_final: 0.7572 (p90) REVERT: A 202 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7451 (mppt) REVERT: A 215 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (t80) REVERT: A 323 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: A 626 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7725 (mt0) REVERT: D 174 LYS cc_start: 0.5197 (mttt) cc_final: 0.4919 (tmmt) REVERT: D 227 GLU cc_start: 0.4920 (OUTLIER) cc_final: 0.3733 (mt-10) REVERT: D 243 TYR cc_start: -0.0320 (OUTLIER) cc_final: -0.1011 (t80) REVERT: D 332 MET cc_start: 0.2244 (ppp) cc_final: 0.1473 (ptm) REVERT: D 408 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.3282 (mmt) REVERT: D 504 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5086 (t80) REVERT: B 325 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7318 (tt) REVERT: B 626 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7435 (mt0) REVERT: B 867 MET cc_start: 0.9228 (mtt) cc_final: 0.8977 (mtt) REVERT: C 243 TYR cc_start: 0.0349 (OUTLIER) cc_final: -0.0334 (t80) REVERT: C 332 MET cc_start: 0.2350 (ppp) cc_final: 0.1476 (ptm) REVERT: C 504 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.4983 (t80) REVERT: C 523 PHE cc_start: 0.3838 (m-80) cc_final: 0.3574 (m-10) REVERT: C 579 MET cc_start: 0.0510 (mtt) cc_final: -0.1433 (mmm) REVERT: K 140 PHE cc_start: 0.7494 (p90) cc_final: 0.7292 (p90) REVERT: K 270 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: K 626 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7499 (mt0) REVERT: K 778 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8370 (mm-30) REVERT: K 821 PHE cc_start: 0.8691 (t80) cc_final: 0.8190 (t80) REVERT: L 332 MET cc_start: 0.2522 (ppp) cc_final: 0.1775 (ptm) REVERT: L 383 MET cc_start: 0.1544 (mtt) cc_final: 0.1324 (mtt) REVERT: L 408 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4433 (mmt) REVERT: L 462 MET cc_start: 0.3990 (mpp) cc_final: 0.3633 (mpm) REVERT: L 579 MET cc_start: 0.0261 (mtt) cc_final: -0.1751 (mmm) outliers start: 85 outliers final: 30 residues processed: 259 average time/residue: 1.0560 time to fit residues: 345.0859 Evaluate side-chains 223 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 177 MET 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 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 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL 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 958 ASN Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 504 PHE 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 205 SER Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 237 PHE Chi-restraints excluded: chain K residue 270 GLN 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 898 MET Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 358 ILE Chi-restraints excluded: chain L residue 408 MET 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 451 optimal weight: 40.0000 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 343 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 chunk 344 optimal weight: 0.6980 chunk 469 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 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** L 373 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.212246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.141390 restraints weight = 87487.820| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 6.31 r_work: 0.3248 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40851 Z= 0.168 Angle : 0.629 32.957 55557 Z= 0.299 Chirality : 0.046 0.765 6345 Planarity : 0.004 0.048 7050 Dihedral : 6.627 59.387 6900 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 1.71 % Allowed : 12.99 % Favored : 85.31 % 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: 0.31 (0.12), residues: 4824 helix: 2.46 (0.12), residues: 1782 sheet: -0.31 (0.19), residues: 738 loop : -1.52 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 271 HIS 0.007 0.001 HIS D 373 PHE 0.038 0.001 PHE D 512 TYR 0.014 0.001 TYR C 50 ARG 0.007 0.000 ARG A 190 *********************** 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 271 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 198 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7792 (p90) cc_final: 0.7576 (p90) REVERT: A 202 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7615 (mppt) REVERT: A 215 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7636 (t80) REVERT: A 323 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: A 626 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7695 (mt0) REVERT: D 174 LYS cc_start: 0.5386 (mttt) cc_final: 0.5051 (tmmt) REVERT: D 227 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4101 (mt-10) REVERT: D 243 TYR cc_start: -0.0561 (OUTLIER) cc_final: -0.1189 (t80) REVERT: D 332 MET cc_start: 0.2211 (ppp) cc_final: 0.1312 (ptm) REVERT: D 504 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5279 (t80) REVERT: B 202 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7798 (mmtm) REVERT: B 325 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7287 (tt) REVERT: B 626 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7441 (mt0) REVERT: B 867 MET cc_start: 0.9212 (mtt) cc_final: 0.8949 (mtt) REVERT: C 115 ARG cc_start: 0.7891 (tpp80) cc_final: 0.7535 (mtp180) REVERT: C 243 TYR cc_start: 0.0053 (OUTLIER) cc_final: -0.0577 (t80) REVERT: C 332 MET cc_start: 0.2260 (ppp) cc_final: 0.1609 (ptm) REVERT: C 504 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5204 (t80) REVERT: C 523 PHE cc_start: 0.3997 (m-80) cc_final: 0.3783 (m-10) REVERT: C 557 MET cc_start: 0.1588 (pp-130) cc_final: 0.1371 (ppp) REVERT: C 579 MET cc_start: 0.1192 (mtt) cc_final: -0.0961 (mmm) REVERT: K 140 PHE cc_start: 0.7544 (p90) cc_final: 0.7333 (p90) REVERT: K 202 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7857 (mptt) REVERT: K 234 ILE cc_start: 0.5540 (mm) cc_final: 0.5330 (tt) REVERT: K 626 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7499 (mt0) REVERT: K 821 PHE cc_start: 0.8689 (t80) cc_final: 0.8191 (t80) REVERT: L 270 MET cc_start: 0.0714 (pmm) cc_final: -0.0533 (ptp) REVERT: L 332 MET cc_start: 0.2583 (ppp) cc_final: 0.1833 (ptm) REVERT: L 408 MET cc_start: 0.5023 (mtt) cc_final: 0.4591 (mmt) REVERT: L 462 MET cc_start: 0.3960 (mpp) cc_final: 0.3590 (mpm) REVERT: L 579 MET cc_start: 0.0686 (mtt) cc_final: -0.1436 (mmm) outliers start: 73 outliers final: 27 residues processed: 257 average time/residue: 1.1241 time to fit residues: 363.1600 Evaluate side-chains 222 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 703 VAL Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 202 LYS 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 958 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 504 PHE 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 225 LEU Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 225 ASP 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 404 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 337 optimal weight: 0.0570 chunk 102 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 339 optimal weight: 8.9990 chunk 411 optimal weight: 1.9990 chunk 435 optimal weight: 6.9990 chunk 431 optimal weight: 30.0000 chunk 197 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 421 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** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.211998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.139651 restraints weight = 87011.668| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 5.62 r_work: 0.3309 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 40851 Z= 0.195 Angle : 0.709 45.698 55557 Z= 0.325 Chirality : 0.047 0.750 6345 Planarity : 0.004 0.041 7050 Dihedral : 6.546 59.477 6900 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 1.87 % Allowed : 13.36 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.12), residues: 4824 helix: 2.42 (0.12), residues: 1785 sheet: -0.30 (0.19), residues: 738 loop : -1.54 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 271 HIS 0.005 0.001 HIS D 373 PHE 0.046 0.001 PHE D 512 TYR 0.018 0.001 TYR D 497 ARG 0.006 0.000 ARG A 190 *********************** 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 280 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7755 (p90) cc_final: 0.7528 (p90) REVERT: A 202 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7650 (mppt) REVERT: A 215 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 323 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: A 626 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7676 (mt0) REVERT: A 884 TRP cc_start: 0.8625 (p90) cc_final: 0.8271 (p90) REVERT: D 152 MET cc_start: -0.2489 (pp-130) cc_final: -0.2713 (pp-130) REVERT: D 227 GLU cc_start: 0.4961 (OUTLIER) cc_final: 0.3860 (mt-10) REVERT: D 243 TYR cc_start: -0.0415 (OUTLIER) cc_final: -0.1072 (t80) REVERT: D 270 MET cc_start: 0.1352 (pmm) cc_final: 0.0542 (pmm) REVERT: D 332 MET cc_start: 0.2145 (ppp) cc_final: 0.1256 (ptm) REVERT: D 504 PHE cc_start: 0.6140 (OUTLIER) cc_final: 0.5176 (t80) REVERT: B 202 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7777 (mptt) REVERT: B 325 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7352 (tt) REVERT: B 626 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7499 (mt0) REVERT: B 867 MET cc_start: 0.9236 (mtt) cc_final: 0.9000 (mtt) REVERT: C 115 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7603 (mtp180) REVERT: C 243 TYR cc_start: 0.0181 (OUTLIER) cc_final: -0.0459 (t80) REVERT: C 332 MET cc_start: 0.2408 (ppp) cc_final: 0.1728 (ptm) REVERT: C 383 MET cc_start: 0.3574 (OUTLIER) cc_final: 0.3359 (mpp) REVERT: C 462 MET cc_start: 0.2640 (ptp) cc_final: 0.1509 (mpm) REVERT: C 504 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.5046 (t80) REVERT: C 523 PHE cc_start: 0.3953 (m-80) cc_final: 0.3739 (m-10) REVERT: C 579 MET cc_start: 0.0529 (mtt) cc_final: -0.1366 (mmm) REVERT: K 140 PHE cc_start: 0.7540 (p90) cc_final: 0.7313 (p90) REVERT: K 202 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7839 (mppt) REVERT: K 626 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7524 (mt0) REVERT: K 821 PHE cc_start: 0.8694 (t80) cc_final: 0.8193 (t80) REVERT: L 62 MET cc_start: 0.1888 (mpp) cc_final: 0.1671 (mtm) REVERT: L 270 MET cc_start: 0.0340 (pmm) cc_final: -0.0102 (pmm) REVERT: L 332 MET cc_start: 0.2437 (ppp) cc_final: 0.1421 (ptm) REVERT: L 408 MET cc_start: 0.4783 (OUTLIER) cc_final: 0.4406 (mmt) REVERT: L 462 MET cc_start: 0.4040 (mpp) cc_final: 0.3621 (mpm) REVERT: L 579 MET cc_start: 0.0580 (mtt) cc_final: -0.1496 (mmm) outliers start: 80 outliers final: 26 residues processed: 263 average time/residue: 1.0551 time to fit residues: 350.2200 Evaluate side-chains 223 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 D residue 90 ASN Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 202 LYS 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 1094 VAL Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 383 MET Chi-restraints excluded: chain C residue 504 PHE 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 225 LEU Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 408 MET Chi-restraints excluded: chain L residue 535 HIS 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 78 optimal weight: 0.6980 chunk 257 optimal weight: 3.9990 chunk 123 optimal weight: 30.0000 chunk 88 optimal weight: 0.9980 chunk 185 optimal weight: 0.3980 chunk 282 optimal weight: 50.0000 chunk 465 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 473 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** 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 194 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.210729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.137613 restraints weight = 87515.280| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 6.23 r_work: 0.3262 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 40851 Z= 0.192 Angle : 0.697 39.831 55557 Z= 0.324 Chirality : 0.047 0.761 6345 Planarity : 0.004 0.042 7050 Dihedral : 6.457 59.376 6900 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.33 % Favored : 94.61 % Rotamer: Outliers : 1.40 % Allowed : 13.97 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 4824 helix: 2.37 (0.12), residues: 1785 sheet: -0.27 (0.19), residues: 738 loop : -1.53 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 271 HIS 0.006 0.001 HIS C 505 PHE 0.054 0.001 PHE D 512 TYR 0.014 0.001 TYR B1065 ARG 0.005 0.000 ARG A 190 *********************** 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 259 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7558 (p90) cc_final: 0.7350 (p90) REVERT: A 202 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7675 (mppt) REVERT: A 323 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: A 626 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7691 (mt0) REVERT: A 884 TRP cc_start: 0.8647 (p90) cc_final: 0.8266 (p90) REVERT: D 88 ILE cc_start: 0.3105 (mt) cc_final: 0.2206 (tp) REVERT: D 227 GLU cc_start: 0.4987 (OUTLIER) cc_final: 0.4073 (mt-10) REVERT: D 243 TYR cc_start: -0.0578 (OUTLIER) cc_final: -0.1176 (t80) REVERT: D 270 MET cc_start: 0.1268 (pmm) cc_final: 0.0555 (pmm) REVERT: D 332 MET cc_start: 0.2563 (ppp) cc_final: 0.1783 (ptm) REVERT: D 504 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5378 (t80) REVERT: B 202 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7707 (mptt) REVERT: B 325 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7237 (tt) REVERT: B 626 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7513 (mt0) REVERT: B 867 MET cc_start: 0.9227 (mtt) cc_final: 0.8988 (mtt) REVERT: C 115 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7714 (mtp180) REVERT: C 243 TYR cc_start: -0.0023 (OUTLIER) cc_final: -0.0575 (t80) REVERT: C 332 MET cc_start: 0.2376 (ppp) cc_final: 0.1572 (ptm) REVERT: C 383 MET cc_start: 0.3462 (OUTLIER) cc_final: 0.3232 (mpp) REVERT: C 460 ARG cc_start: 0.4677 (OUTLIER) cc_final: 0.4425 (ttm110) REVERT: C 523 PHE cc_start: 0.3904 (m-80) cc_final: 0.3703 (m-10) REVERT: C 579 MET cc_start: 0.1492 (mtt) cc_final: -0.0752 (mmm) REVERT: K 202 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7799 (mppt) REVERT: K 626 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7535 (mt0) REVERT: K 821 PHE cc_start: 0.8660 (t80) cc_final: 0.8155 (t80) REVERT: L 88 ILE cc_start: 0.2615 (mt) cc_final: 0.2089 (tp) REVERT: L 270 MET cc_start: 0.0400 (pmm) cc_final: 0.0053 (pmm) REVERT: L 332 MET cc_start: 0.2335 (ppp) cc_final: 0.1469 (ptm) REVERT: L 408 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.4655 (mmt) REVERT: L 462 MET cc_start: 0.3830 (mpp) cc_final: 0.3488 (mpm) REVERT: L 579 MET cc_start: 0.1445 (mtt) cc_final: -0.0956 (mmm) outliers start: 60 outliers final: 25 residues processed: 247 average time/residue: 1.0991 time to fit residues: 340.3848 Evaluate side-chains 223 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 202 LYS 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 1094 VAL 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 383 MET Chi-restraints excluded: chain C residue 460 ARG 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 225 LEU Chi-restraints excluded: chain K residue 585 ILE Chi-restraints excluded: chain K residue 736 CYS Chi-restraints excluded: chain K residue 898 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 408 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 340 optimal weight: 9.9990 chunk 426 optimal weight: 6.9990 chunk 383 optimal weight: 0.4980 chunk 170 optimal weight: 20.0000 chunk 160 optimal weight: 50.0000 chunk 194 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 453 optimal weight: 20.0000 chunk 304 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** 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** B 899 GLN C 373 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.210484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.133049 restraints weight = 86887.824| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.75 r_work: 0.3325 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.175 40851 Z= 0.532 Angle : 0.798 68.099 55557 Z= 0.377 Chirality : 0.053 1.045 6345 Planarity : 0.004 0.054 7050 Dihedral : 6.503 59.992 6900 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 1.26 % Allowed : 14.41 % Favored : 84.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.12 (0.12), residues: 4824 helix: 2.24 (0.12), residues: 1785 sheet: -0.35 (0.19), residues: 738 loop : -1.60 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 271 HIS 0.046 0.001 HIS L 535 PHE 0.071 0.002 PHE D 512 TYR 0.024 0.002 TYR K1065 ARG 0.013 0.001 ARG C 460 ********************** 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: 54 poor density : 190 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7664 (p90) cc_final: 0.7443 (p90) REVERT: A 202 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7689 (mppt) REVERT: A 228 LEU cc_start: 0.7524 (mt) cc_final: 0.7302 (mp) REVERT: A 323 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: A 626 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7787 (mt0) REVERT: D 88 ILE cc_start: 0.2477 (mt) cc_final: 0.1836 (tp) REVERT: D 227 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.3713 (mt-10) REVERT: D 243 TYR cc_start: -0.0397 (OUTLIER) cc_final: -0.1049 (t80) REVERT: D 270 MET cc_start: 0.1024 (pmm) cc_final: 0.0451 (pmm) REVERT: D 332 MET cc_start: 0.2288 (ppp) cc_final: 0.1482 (ptm) REVERT: D 504 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5158 (t80) REVERT: B 202 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7749 (mptt) REVERT: B 325 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 626 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7628 (mt0) REVERT: C 243 TYR cc_start: 0.0225 (OUTLIER) cc_final: -0.0447 (t80) REVERT: C 332 MET cc_start: 0.2443 (ppp) cc_final: 0.1726 (ptm) REVERT: C 383 MET cc_start: 0.3630 (OUTLIER) cc_final: 0.3336 (mpp) REVERT: C 523 PHE cc_start: 0.3823 (m-80) cc_final: 0.3580 (m-10) REVERT: C 579 MET cc_start: 0.0453 (mtt) cc_final: -0.1390 (mmm) REVERT: K 202 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7915 (mptt) REVERT: K 626 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7616 (mt0) REVERT: K 821 PHE cc_start: 0.8707 (t80) cc_final: 0.8262 (t80) REVERT: L 88 ILE cc_start: 0.1727 (mt) cc_final: 0.1348 (tp) REVERT: L 270 MET cc_start: 0.0278 (pmm) cc_final: -0.0131 (pmm) REVERT: L 332 MET cc_start: 0.2398 (ppp) cc_final: 0.1385 (ptm) REVERT: L 408 MET cc_start: 0.4773 (OUTLIER) cc_final: 0.4374 (mmt) REVERT: L 462 MET cc_start: 0.4050 (mpp) cc_final: 0.3550 (mpm) REVERT: L 579 MET cc_start: 0.0472 (mtt) cc_final: -0.1551 (mmm) outliers start: 54 outliers final: 28 residues processed: 234 average time/residue: 1.0756 time to fit residues: 317.0467 Evaluate side-chains 225 residues out of total 4281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL 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 227 GLU Chi-restraints excluded: chain D residue 243 TYR Chi-restraints excluded: chain D residue 504 PHE Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 202 LYS 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 958 ASN Chi-restraints excluded: chain B residue 1094 VAL 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 383 MET 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 225 LEU Chi-restraints excluded: chain K residue 325 ILE 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 898 MET Chi-restraints excluded: chain L residue 82 MET Chi-restraints excluded: chain L residue 90 ASN Chi-restraints excluded: chain L residue 408 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 419 optimal weight: 0.7980 chunk 421 optimal weight: 0.8980 chunk 289 optimal weight: 40.0000 chunk 106 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 442 optimal weight: 4.9990 chunk 270 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** 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** B 899 GLN C 508 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.211403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137978 restraints weight = 87415.468| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 5.79 r_work: 0.3230 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 40851 Z= 0.253 Angle : 0.733 36.547 55557 Z= 0.346 Chirality : 0.047 0.746 6345 Planarity : 0.004 0.053 7050 Dihedral : 6.457 59.629 6900 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 1.12 % Allowed : 14.62 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.23 (0.12), residues: 1791 sheet: -0.30 (0.19), residues: 738 loop : -1.59 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 271 HIS 0.012 0.001 HIS L 535 PHE 0.063 0.001 PHE D 512 TYR 0.016 0.001 TYR B1065 ARG 0.007 0.000 ARG K 565 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38276.81 seconds wall clock time: 651 minutes 8.18 seconds (39068.18 seconds total)