Starting phenix.real_space_refine on Thu Feb 22 19:53:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm7_27529/02_2024/8dm7_27529.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 175 5.16 5 C 22417 2.51 5 N 5791 2.21 5 O 6782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35165 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "B" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} Chain: "E" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4833 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 27, 'TRANS': 565} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" 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: "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 Time building chain proxies: 17.94, per 1000 atoms: 0.51 Number of scatterers: 35165 At special positions: 0 Unit cell: (136, 159, 237, 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 175 16.00 O 6782 8.00 N 5791 7.00 C 22417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 546 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1074 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 122 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1098 " " NAG W 1 " - " ASN C1134 " Time building additional restraints: 13.39 Conformation dependent library (CDL) restraints added in 5.8 seconds 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8146 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 54 sheets defined 38.0% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.679A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.279A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.649A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.859A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.131A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.728A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.312A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.023A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.645A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 856 removed outlier: 3.684A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.713A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.887A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.917A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.124A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.967A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.821A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.613A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 4.175A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.756A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.056A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.147A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.081A pdb=" N GLN D 34 " --> pdb=" O ASN D 30 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.824A pdb=" N GLU D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.685A pdb=" N SER D 106 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 5.019A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.672A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) 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 218 through 231 removed outlier: 3.611A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.711A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.632A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.712A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.876A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.676A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.435A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) 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 removed outlier: 3.614A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.700A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.307A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 4.036A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 598 Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.571A pdb=" N GLN E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.850A pdb=" N GLU E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.694A pdb=" N SER E 106 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.978A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.717A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 231 removed outlier: 3.660A pdb=" N LEU E 222 " --> pdb=" O ASN E 218 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.729A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.637A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.897A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.669A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.456A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.552A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.688A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.329A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 4.039A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 575 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.716A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.557A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.793A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.837A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.822A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.988A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.688A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.440A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.319A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.666A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.984A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.676A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.819A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.631A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.853A pdb=" N ALA B 435 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.940A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.653A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.420A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.343A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.870A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.002A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.203A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.002A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.906A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.312A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AF8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.849A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.327A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1691 hydrogen bonds defined for protein. 4773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.04 Time building geometry restraints manager: 14.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11169 1.35 - 1.47: 9441 1.47 - 1.60: 15155 1.60 - 1.73: 0 1.73 - 1.85: 247 Bond restraints: 36012 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.94e+00 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.38e-02 5.25e+03 6.59e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 36007 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.50: 836 105.50 - 112.66: 18408 112.66 - 119.82: 12197 119.82 - 126.98: 17065 126.98 - 134.13: 459 Bond angle restraints: 48965 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.83 -7.37 1.41e+00 5.03e-01 2.73e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.81 121.21 -11.40 2.21e+00 2.05e-01 2.66e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.51e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 ... (remaining 48960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 20295 17.73 - 35.45: 1523 35.45 - 53.18: 302 53.18 - 70.91: 75 70.91 - 88.63: 36 Dihedral angle restraints: 22231 sinusoidal: 9581 harmonic: 12650 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.28 38.72 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.15 37.85 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -50.83 -35.17 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 22228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4355 0.064 - 0.128: 1037 0.128 - 0.192: 180 0.192 - 0.256: 15 0.256 - 0.320: 1 Chirality restraints: 5588 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE D 291 " pdb=" CA ILE D 291 " pdb=" CG1 ILE D 291 " pdb=" CG2 ILE D 291 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU C 858 " pdb=" CB LEU C 858 " pdb=" CD1 LEU C 858 " pdb=" CD2 LEU C 858 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 5585 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 594 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLY A 594 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 594 " -0.022 2.00e-02 2.50e+03 pdb=" N VAL A 595 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 952 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C VAL A 952 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL A 952 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 953 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 954 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C HIS A 954 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS A 954 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 955 " -0.018 2.00e-02 2.50e+03 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9903 2.82 - 3.34: 30555 3.34 - 3.86: 60176 3.86 - 4.38: 69556 4.38 - 4.90: 119826 Nonbonded interactions: 290016 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.310 2.440 nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.310 2.440 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.313 2.440 ... (remaining 290011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.260 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 93.570 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.460 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.005 0.069 36012 Z= 0.319 Angle : 0.838 11.403 48965 Z= 0.470 Chirality : 0.056 0.320 5588 Planarity : 0.007 0.070 6257 Dihedral : 13.316 88.635 13947 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.58 % Allowed : 3.51 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 4278 helix: 1.26 (0.12), residues: 1424 sheet: 0.80 (0.18), residues: 703 loop : -0.51 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 886 HIS 0.019 0.002 HIS C 954 PHE 0.027 0.002 PHE A 377 TYR 0.035 0.002 TYR D 385 ARG 0.016 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 469 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7736 (tm130) REVERT: A 342 PHE cc_start: 0.7970 (m-80) cc_final: 0.7769 (m-80) REVERT: A 371 PHE cc_start: 0.4326 (OUTLIER) cc_final: 0.4057 (m-80) REVERT: A 448 ASN cc_start: 0.6341 (t0) cc_final: 0.6133 (t0) REVERT: B 740 MET cc_start: 0.8329 (ttt) cc_final: 0.8116 (ttm) REVERT: C 54 LEU cc_start: 0.8902 (mt) cc_final: 0.8621 (mp) REVERT: C 177 MET cc_start: 0.6643 (pmm) cc_final: 0.6182 (ppp) REVERT: C 245 HIS cc_start: 0.6681 (m90) cc_final: 0.6137 (m90) REVERT: D 157 ASP cc_start: 0.0229 (t0) cc_final: 0.0029 (t0) REVERT: D 216 ASN cc_start: 0.4784 (m-40) cc_final: 0.4444 (m-40) REVERT: D 249 MET cc_start: 0.0422 (ttm) cc_final: 0.0081 (tmt) REVERT: D 298 MET cc_start: 0.2317 (mmm) cc_final: 0.1920 (ptt) REVERT: D 322 HIS cc_start: 0.6514 (m-70) cc_final: 0.5915 (m-70) REVERT: D 323 MET cc_start: 0.0222 (mmm) cc_final: -0.1299 (mmm) REVERT: D 332 MET cc_start: 0.2830 (ptm) cc_final: 0.2564 (ppp) REVERT: D 341 LYS cc_start: 0.7357 (mmmm) cc_final: 0.6774 (mppt) REVERT: D 360 MET cc_start: 0.1996 (ttm) cc_final: 0.1330 (ttm) REVERT: D 535 TYR cc_start: 0.0060 (t80) cc_final: -0.0532 (p90) REVERT: E 26 LYS cc_start: 0.6760 (mtpt) cc_final: 0.6510 (mmtt) REVERT: E 62 MET cc_start: 0.3354 (ttp) cc_final: 0.2852 (tpt) REVERT: E 98 GLN cc_start: 0.5556 (mt0) cc_final: 0.5228 (mm110) REVERT: E 135 PRO cc_start: 0.2066 (Cg_endo) cc_final: 0.1335 (Cg_exo) REVERT: E 165 TRP cc_start: 0.0369 (t60) cc_final: -0.0735 (m-90) REVERT: E 189 GLU cc_start: 0.4525 (mm-30) cc_final: 0.4179 (mm-30) REVERT: E 246 ARG cc_start: 0.1689 (ttp-110) cc_final: 0.1098 (tmm-80) REVERT: E 249 MET cc_start: 0.2490 (ttm) cc_final: 0.2060 (tpp) REVERT: E 270 MET cc_start: -0.1758 (tpt) cc_final: -0.2184 (tpt) REVERT: E 298 MET cc_start: 0.1731 (mmm) cc_final: 0.0648 (tmm) REVERT: E 328 TRP cc_start: 0.4405 (m100) cc_final: 0.3593 (t-100) REVERT: E 418 LEU cc_start: 0.1073 (mt) cc_final: 0.0815 (mt) REVERT: E 435 GLU cc_start: -0.0319 (mm-30) cc_final: -0.0694 (pt0) REVERT: E 546 ASN cc_start: 0.2596 (m110) cc_final: 0.1243 (t0) REVERT: E 558 LEU cc_start: -0.0489 (mp) cc_final: -0.0785 (pp) outliers start: 22 outliers final: 1 residues processed: 485 average time/residue: 1.4198 time to fit residues: 831.3722 Evaluate side-chains 216 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain B residue 371 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 363 optimal weight: 0.6980 chunk 325 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 204 optimal weight: 0.6980 chunk 250 optimal weight: 0.7980 chunk 390 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 66 HIS A 115 GLN A 360 ASN A 613 GLN A 957 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 613 GLN B 755 GLN B 824 ASN C 134 GLN C 856 ASN C 913 GLN C 926 GLN D 76 GLN D 117 ASN D 239 HIS D 345 HIS D 368 ASN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 98 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36012 Z= 0.183 Angle : 0.558 13.976 48965 Z= 0.289 Chirality : 0.043 0.268 5588 Planarity : 0.004 0.044 6257 Dihedral : 6.661 59.038 5946 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.58 % Allowed : 9.39 % Favored : 89.02 % 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: 0.87 (0.12), residues: 4278 helix: 1.77 (0.13), residues: 1444 sheet: 0.78 (0.18), residues: 695 loop : -0.29 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 258 HIS 0.009 0.001 HIS D 505 PHE 0.033 0.001 PHE D 369 TYR 0.023 0.001 TYR B1067 ARG 0.009 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 246 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7694 (tm130) REVERT: A 448 ASN cc_start: 0.6407 (t0) cc_final: 0.6133 (t0) REVERT: A 740 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7420 (ttp) REVERT: A 787 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8151 (mm-40) REVERT: A 1050 MET cc_start: 0.9091 (ptm) cc_final: 0.8853 (ptp) REVERT: B 740 MET cc_start: 0.8317 (ttt) cc_final: 0.8089 (ttm) REVERT: C 177 MET cc_start: 0.6756 (pmm) cc_final: 0.6316 (ppp) REVERT: C 245 HIS cc_start: 0.6616 (m90) cc_final: 0.6067 (m-70) REVERT: C 258 TRP cc_start: 0.6575 (m-90) cc_final: 0.6362 (m-90) REVERT: C 517 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5263 (tm) REVERT: C 1010 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: D 249 MET cc_start: 0.0300 (ttm) cc_final: -0.0010 (tmt) REVERT: D 298 MET cc_start: 0.2356 (mmm) cc_final: 0.1952 (ptt) REVERT: D 341 LYS cc_start: 0.7394 (mmmm) cc_final: 0.6748 (mppt) REVERT: D 360 MET cc_start: 0.2086 (ttm) cc_final: 0.1545 (ttm) REVERT: D 483 GLU cc_start: 0.5795 (tp30) cc_final: 0.5363 (pt0) REVERT: D 535 TYR cc_start: 0.0137 (t80) cc_final: -0.0580 (p90) REVERT: E 28 PHE cc_start: 0.4490 (t80) cc_final: 0.4223 (t80) REVERT: E 62 MET cc_start: 0.3236 (ttp) cc_final: 0.2738 (tpt) REVERT: E 95 ARG cc_start: 0.2081 (ptp-110) cc_final: 0.1655 (tpp-160) REVERT: E 98 GLN cc_start: 0.5909 (mt0) cc_final: 0.5658 (mm110) REVERT: E 163 TRP cc_start: 0.3261 (m-90) cc_final: 0.2764 (m-90) REVERT: E 165 TRP cc_start: 0.0199 (t60) cc_final: -0.0692 (m-90) REVERT: E 246 ARG cc_start: 0.1569 (ttp-110) cc_final: 0.0969 (tmm-80) REVERT: E 249 MET cc_start: 0.2649 (ttm) cc_final: 0.2208 (tpp) REVERT: E 271 TRP cc_start: 0.1424 (OUTLIER) cc_final: 0.1111 (m-90) REVERT: E 298 MET cc_start: 0.1471 (mmm) cc_final: 0.0507 (tmm) REVERT: E 328 TRP cc_start: 0.4696 (m100) cc_final: 0.3556 (t-100) REVERT: E 462 MET cc_start: 0.1207 (OUTLIER) cc_final: 0.0208 (ttt) REVERT: E 546 ASN cc_start: 0.2225 (m110) cc_final: 0.1602 (p0) REVERT: E 558 LEU cc_start: -0.0456 (mp) cc_final: -0.0717 (mt) outliers start: 60 outliers final: 13 residues processed: 286 average time/residue: 1.2536 time to fit residues: 444.8856 Evaluate side-chains 212 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 462 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 217 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 chunk 422 optimal weight: 4.9990 chunk 348 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 313 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 603 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN C 314 GLN C 317 ASN C 394 ASN C 824 ASN D 76 GLN D 239 HIS D 472 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 36012 Z= 0.668 Angle : 0.794 15.890 48965 Z= 0.410 Chirality : 0.055 0.298 5588 Planarity : 0.006 0.065 6257 Dihedral : 7.051 59.160 5946 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.53 % Allowed : 11.32 % Favored : 86.15 % 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: 0.33 (0.12), residues: 4278 helix: 1.19 (0.13), residues: 1449 sheet: 0.38 (0.17), residues: 766 loop : -0.49 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 886 HIS 0.020 0.003 HIS E 540 PHE 0.037 0.003 PHE D 369 TYR 0.039 0.003 TYR A 200 ARG 0.012 0.001 ARG E 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 216 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 PHE cc_start: 0.4754 (OUTLIER) cc_final: 0.4519 (t80) REVERT: A 740 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7416 (ttp) REVERT: B 129 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6046 (mtmm) REVERT: B 533 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8177 (tt) REVERT: B 740 MET cc_start: 0.8466 (ttt) cc_final: 0.8205 (ttm) REVERT: C 177 MET cc_start: 0.7014 (pmm) cc_final: 0.6766 (ppp) REVERT: C 200 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.7059 (t80) REVERT: C 1010 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: D 298 MET cc_start: 0.1978 (mmm) cc_final: 0.1386 (ptt) REVERT: D 340 ARG cc_start: 0.3531 (OUTLIER) cc_final: 0.2892 (ptt-90) REVERT: D 341 LYS cc_start: 0.7355 (mmmm) cc_final: 0.6747 (mppt) REVERT: D 408 MET cc_start: 0.3826 (mmp) cc_final: 0.2964 (tpt) REVERT: D 483 GLU cc_start: 0.5894 (tp30) cc_final: 0.5378 (pt0) REVERT: D 494 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.4855 (t0) REVERT: D 535 TYR cc_start: 0.0501 (t80) cc_final: -0.0396 (p90) REVERT: E 62 MET cc_start: 0.3158 (ttp) cc_final: 0.2680 (tpt) REVERT: E 95 ARG cc_start: 0.1926 (ptp-110) cc_final: 0.1666 (ttm110) REVERT: E 144 LEU cc_start: 0.0340 (tm) cc_final: -0.0659 (pt) REVERT: E 165 TRP cc_start: 0.0509 (t60) cc_final: 0.0284 (t60) REVERT: E 246 ARG cc_start: 0.1311 (ttp-110) cc_final: 0.0713 (tmm-80) REVERT: E 249 MET cc_start: 0.2474 (ttm) cc_final: 0.2020 (tpp) REVERT: E 275 TRP cc_start: 0.4120 (m-10) cc_final: 0.3448 (m-10) REVERT: E 298 MET cc_start: 0.1705 (mmm) cc_final: 0.0485 (tmm) REVERT: E 328 TRP cc_start: 0.4589 (m100) cc_final: 0.3704 (t-100) REVERT: E 332 MET cc_start: 0.3286 (ptm) cc_final: 0.3024 (ptm) REVERT: E 366 MET cc_start: -0.0637 (tpt) cc_final: -0.1190 (tpt) REVERT: E 479 GLU cc_start: 0.2810 (pp20) cc_final: 0.1368 (pt0) REVERT: E 546 ASN cc_start: 0.2511 (m110) cc_final: 0.1602 (t0) outliers start: 96 outliers final: 34 residues processed: 290 average time/residue: 1.3395 time to fit residues: 476.4386 Evaluate side-chains 218 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 315 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 386 optimal weight: 2.9990 chunk 294 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 392 optimal weight: 20.0000 chunk 415 optimal weight: 9.9990 chunk 205 optimal weight: 0.0770 chunk 372 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 448 ASN A 762 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 613 GLN D 239 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 36012 Z= 0.206 Angle : 0.561 14.642 48965 Z= 0.289 Chirality : 0.044 0.209 5588 Planarity : 0.004 0.054 6257 Dihedral : 6.342 59.273 5946 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.95 % Allowed : 13.38 % Favored : 84.67 % 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: 0.68 (0.12), residues: 4278 helix: 1.67 (0.14), residues: 1424 sheet: 0.44 (0.17), residues: 720 loop : -0.34 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 165 HIS 0.009 0.001 HIS D 239 PHE 0.025 0.001 PHE D 369 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.000 ARG C 577 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 192 time to evaluate : 4.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7838 (tm130) REVERT: A 258 TRP cc_start: 0.5790 (m-90) cc_final: 0.5305 (m-90) REVERT: A 371 PHE cc_start: 0.4643 (OUTLIER) cc_final: 0.4382 (t80) REVERT: A 740 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7376 (ttp) REVERT: A 855 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7059 (t80) REVERT: B 533 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 740 MET cc_start: 0.8398 (ttt) cc_final: 0.8133 (ttm) REVERT: C 245 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.6135 (m90) REVERT: C 540 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6971 (p0) REVERT: D 298 MET cc_start: 0.2429 (mmm) cc_final: 0.1947 (ptt) REVERT: D 340 ARG cc_start: 0.3602 (OUTLIER) cc_final: 0.3132 (ptt-90) REVERT: D 341 LYS cc_start: 0.7339 (mmmm) cc_final: 0.6761 (mppt) REVERT: D 408 MET cc_start: 0.3919 (mmp) cc_final: 0.3010 (tpt) REVERT: D 483 GLU cc_start: 0.5913 (tp30) cc_final: 0.5421 (pt0) REVERT: D 535 TYR cc_start: 0.0829 (t80) cc_final: -0.0435 (p90) REVERT: D 579 MET cc_start: -0.1022 (OUTLIER) cc_final: -0.1304 (mtt) REVERT: E 62 MET cc_start: 0.3242 (ttp) cc_final: 0.2703 (tpt) REVERT: E 95 ARG cc_start: 0.2191 (ptp-110) cc_final: 0.1990 (ptm160) REVERT: E 144 LEU cc_start: 0.0542 (tm) cc_final: -0.0074 (pp) REVERT: E 165 TRP cc_start: 0.0386 (t60) cc_final: 0.0171 (t60) REVERT: E 246 ARG cc_start: 0.1287 (ttp-110) cc_final: 0.0817 (tmm-80) REVERT: E 249 MET cc_start: 0.2406 (ttm) cc_final: 0.1960 (tpp) REVERT: E 271 TRP cc_start: 0.1291 (OUTLIER) cc_final: 0.1037 (m-90) REVERT: E 275 TRP cc_start: 0.3981 (m-10) cc_final: 0.3388 (m-10) REVERT: E 298 MET cc_start: 0.1603 (mmm) cc_final: 0.0470 (tmm) REVERT: E 328 TRP cc_start: 0.4513 (m100) cc_final: 0.3591 (t-100) REVERT: E 332 MET cc_start: 0.3195 (ptm) cc_final: 0.2820 (ptm) REVERT: E 366 MET cc_start: -0.0116 (tpt) cc_final: -0.0893 (tpt) REVERT: E 480 MET cc_start: 0.2646 (ptp) cc_final: 0.2294 (ptt) REVERT: E 546 ASN cc_start: 0.2511 (m110) cc_final: 0.1582 (t0) outliers start: 74 outliers final: 27 residues processed: 248 average time/residue: 1.3059 time to fit residues: 404.0229 Evaluate side-chains 203 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 346 optimal weight: 9.9990 chunk 235 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 309 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 354 optimal weight: 10.0000 chunk 287 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 373 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 544 ASN C 872 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 36012 Z= 0.574 Angle : 0.720 14.848 48965 Z= 0.368 Chirality : 0.051 0.321 5588 Planarity : 0.005 0.049 6257 Dihedral : 6.634 59.949 5946 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.80 % Allowed : 13.43 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.12), residues: 4278 helix: 1.24 (0.13), residues: 1434 sheet: 0.21 (0.18), residues: 750 loop : -0.53 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.010 0.002 HIS C 954 PHE 0.030 0.002 PHE D 369 TYR 0.029 0.003 TYR B1067 ARG 0.010 0.001 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 171 time to evaluate : 4.210 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 125 ASN cc_start: 0.6232 (p0) cc_final: 0.5787 (m-40) REVERT: A 258 TRP cc_start: 0.5783 (m-90) cc_final: 0.5183 (m-90) REVERT: A 740 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: A 780 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: B 129 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6589 (mtmm) REVERT: B 533 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8196 (tt) REVERT: B 740 MET cc_start: 0.8443 (ttt) cc_final: 0.8204 (ttm) REVERT: C 740 MET cc_start: 0.8358 (ttp) cc_final: 0.7916 (ttp) REVERT: D 298 MET cc_start: 0.2408 (mmm) cc_final: 0.1811 (ptt) REVERT: D 408 MET cc_start: 0.3972 (mmp) cc_final: 0.3088 (tpt) REVERT: D 483 GLU cc_start: 0.5884 (tp30) cc_final: 0.5434 (pt0) REVERT: D 494 ASP cc_start: 0.5716 (OUTLIER) cc_final: 0.4811 (t0) REVERT: D 535 TYR cc_start: 0.0936 (t80) cc_final: -0.0637 (p90) REVERT: D 579 MET cc_start: -0.1133 (mmm) cc_final: -0.1403 (mtt) REVERT: E 22 GLU cc_start: 0.2462 (tt0) cc_final: 0.1818 (mm-30) REVERT: E 62 MET cc_start: 0.3364 (ttp) cc_final: 0.2819 (tpt) REVERT: E 95 ARG cc_start: 0.1963 (ptp-110) cc_final: 0.1487 (tpp-160) REVERT: E 144 LEU cc_start: 0.0849 (tm) cc_final: -0.0027 (pp) REVERT: E 165 TRP cc_start: 0.0074 (t60) cc_final: -0.0767 (m-90) REVERT: E 246 ARG cc_start: 0.1190 (ttp-110) cc_final: 0.0552 (tmm-80) REVERT: E 249 MET cc_start: 0.2316 (ttm) cc_final: 0.1876 (tpp) REVERT: E 271 TRP cc_start: 0.1261 (OUTLIER) cc_final: 0.0968 (m-90) REVERT: E 298 MET cc_start: 0.1521 (mmm) cc_final: 0.0470 (tmm) REVERT: E 328 TRP cc_start: 0.4500 (m100) cc_final: 0.3768 (t-100) REVERT: E 332 MET cc_start: 0.3095 (ptm) cc_final: 0.2747 (ptm) REVERT: E 388 GLN cc_start: 0.4034 (mm-40) cc_final: 0.3689 (mm-40) REVERT: E 482 ARG cc_start: 0.4310 (ptt90) cc_final: 0.3662 (mtt180) REVERT: E 534 LYS cc_start: 0.3968 (mppt) cc_final: 0.3618 (mppt) REVERT: E 546 ASN cc_start: 0.2784 (m110) cc_final: 0.1927 (t0) outliers start: 106 outliers final: 51 residues processed: 262 average time/residue: 1.2143 time to fit residues: 399.5469 Evaluate side-chains 216 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 139 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 416 optimal weight: 3.9990 chunk 345 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 544 ASN C 856 ASN D 113 ASN D 330 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 36012 Z= 0.381 Angle : 0.614 14.355 48965 Z= 0.314 Chirality : 0.046 0.268 5588 Planarity : 0.004 0.047 6257 Dihedral : 6.226 58.103 5944 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.32 % Allowed : 14.22 % Favored : 83.46 % 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: 0.38 (0.12), residues: 4278 helix: 1.39 (0.13), residues: 1446 sheet: 0.29 (0.18), residues: 725 loop : -0.52 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.010 0.001 HIS E 374 PHE 0.022 0.002 PHE D 369 TYR 0.025 0.002 TYR B1067 ARG 0.005 0.000 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 171 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6238 (p0) cc_final: 0.5902 (m-40) REVERT: A 740 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7377 (ttp) REVERT: A 780 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: A 855 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7167 (t80) REVERT: B 533 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8277 (tt) REVERT: B 740 MET cc_start: 0.8429 (ttt) cc_final: 0.8170 (ttm) REVERT: D 45 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6752 (pp) REVERT: D 89 GLN cc_start: 0.4406 (mp10) cc_final: 0.3225 (tp40) REVERT: D 298 MET cc_start: 0.2242 (mmm) cc_final: 0.1792 (ptt) REVERT: D 408 MET cc_start: 0.3794 (mmp) cc_final: 0.2913 (tpt) REVERT: D 483 GLU cc_start: 0.5887 (tp30) cc_final: 0.5427 (pt0) REVERT: D 494 ASP cc_start: 0.5862 (OUTLIER) cc_final: 0.4949 (t0) REVERT: D 535 TYR cc_start: 0.1104 (t80) cc_final: -0.0623 (p90) REVERT: D 579 MET cc_start: -0.0600 (OUTLIER) cc_final: -0.0816 (mtt) REVERT: E 62 MET cc_start: 0.3329 (ttp) cc_final: 0.2834 (tpt) REVERT: E 144 LEU cc_start: 0.0368 (tm) cc_final: -0.0486 (pp) REVERT: E 246 ARG cc_start: 0.1197 (ttp-110) cc_final: 0.0585 (tmm-80) REVERT: E 249 MET cc_start: 0.2332 (ttm) cc_final: 0.1884 (tpp) REVERT: E 271 TRP cc_start: 0.1414 (OUTLIER) cc_final: 0.1121 (m-90) REVERT: E 298 MET cc_start: 0.1430 (mmm) cc_final: 0.0408 (tmm) REVERT: E 323 MET cc_start: 0.1452 (tpp) cc_final: 0.0921 (tpp) REVERT: E 328 TRP cc_start: 0.4417 (m100) cc_final: 0.3696 (t-100) REVERT: E 332 MET cc_start: 0.3103 (ptm) cc_final: 0.2685 (ptm) REVERT: E 482 ARG cc_start: 0.4300 (ptt90) cc_final: 0.3663 (mtt180) REVERT: E 546 ASN cc_start: 0.2743 (m110) cc_final: 0.1910 (t0) outliers start: 88 outliers final: 48 residues processed: 243 average time/residue: 1.2122 time to fit residues: 369.6915 Evaluate side-chains 213 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 401 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 235 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 414 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 36012 Z= 0.465 Angle : 0.671 14.181 48965 Z= 0.342 Chirality : 0.048 0.311 5588 Planarity : 0.004 0.051 6257 Dihedral : 6.262 58.994 5944 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.45 % Allowed : 14.72 % Favored : 82.82 % 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: 0.20 (0.12), residues: 4278 helix: 1.24 (0.13), residues: 1446 sheet: 0.16 (0.18), residues: 721 loop : -0.62 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.011 0.002 HIS E 374 PHE 0.024 0.002 PHE D 369 TYR 0.026 0.002 TYR B1067 ARG 0.009 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 169 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 125 ASN cc_start: 0.6258 (p0) cc_final: 0.5810 (m-40) REVERT: A 177 MET cc_start: 0.5699 (pmm) cc_final: 0.4418 (ppp) REVERT: A 780 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: B 740 MET cc_start: 0.8432 (ttt) cc_final: 0.8178 (ttm) REVERT: C 740 MET cc_start: 0.8365 (ttp) cc_final: 0.7903 (ttp) REVERT: D 45 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6817 (pp) REVERT: D 89 GLN cc_start: 0.4462 (mp10) cc_final: 0.3287 (tp40) REVERT: D 298 MET cc_start: 0.2414 (mmm) cc_final: 0.1969 (ptt) REVERT: D 408 MET cc_start: 0.3574 (mmp) cc_final: 0.2619 (tpt) REVERT: D 483 GLU cc_start: 0.5878 (tp30) cc_final: 0.5432 (pt0) REVERT: D 494 ASP cc_start: 0.5890 (OUTLIER) cc_final: 0.5075 (t0) REVERT: D 535 TYR cc_start: 0.1164 (t80) cc_final: -0.0688 (p90) REVERT: D 579 MET cc_start: -0.0566 (OUTLIER) cc_final: -0.0828 (mtt) REVERT: E 22 GLU cc_start: 0.2583 (tt0) cc_final: 0.1889 (mm-30) REVERT: E 57 GLU cc_start: 0.2795 (OUTLIER) cc_final: 0.2437 (pt0) REVERT: E 62 MET cc_start: 0.3426 (ttp) cc_final: 0.2910 (tpt) REVERT: E 144 LEU cc_start: 0.0340 (tm) cc_final: -0.0546 (pp) REVERT: E 246 ARG cc_start: 0.1254 (ttp-110) cc_final: 0.0560 (tmm-80) REVERT: E 249 MET cc_start: 0.2309 (ttm) cc_final: 0.1857 (tpp) REVERT: E 271 TRP cc_start: 0.1172 (OUTLIER) cc_final: 0.0945 (m-90) REVERT: E 298 MET cc_start: 0.1043 (mmm) cc_final: 0.0026 (tmm) REVERT: E 323 MET cc_start: 0.1523 (tpp) cc_final: 0.0841 (tpp) REVERT: E 328 TRP cc_start: 0.4219 (m100) cc_final: 0.3701 (t-100) REVERT: E 332 MET cc_start: 0.3064 (ptm) cc_final: 0.2563 (ptm) REVERT: E 482 ARG cc_start: 0.4675 (ptt90) cc_final: 0.3846 (mtt180) REVERT: E 546 ASN cc_start: 0.2650 (m110) cc_final: 0.1886 (t0) outliers start: 93 outliers final: 57 residues processed: 246 average time/residue: 1.1979 time to fit residues: 371.7002 Evaluate side-chains 224 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 163 TRP Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 431 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 256 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 282 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 188 ASN ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 36012 Z= 0.189 Angle : 0.566 13.466 48965 Z= 0.287 Chirality : 0.043 0.231 5588 Planarity : 0.004 0.052 6257 Dihedral : 5.823 59.293 5944 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.98 % Allowed : 15.36 % Favored : 82.66 % 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: 0.45 (0.13), residues: 4278 helix: 1.48 (0.14), residues: 1450 sheet: 0.25 (0.18), residues: 714 loop : -0.47 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 606 HIS 0.008 0.001 HIS D 239 PHE 0.020 0.001 PHE C 565 TYR 0.026 0.001 TYR D 199 ARG 0.004 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 166 time to evaluate : 3.869 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 125 ASN cc_start: 0.6172 (p0) cc_final: 0.5831 (m-40) REVERT: A 177 MET cc_start: 0.6023 (pmm) cc_final: 0.4833 (ppp) REVERT: A 740 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7408 (ttp) REVERT: A 780 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: B 740 MET cc_start: 0.8381 (ttt) cc_final: 0.8116 (ttm) REVERT: C 200 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7540 (t80) REVERT: D 45 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6802 (pp) REVERT: D 298 MET cc_start: 0.2662 (mmm) cc_final: 0.2115 (ptt) REVERT: D 408 MET cc_start: 0.3690 (mmp) cc_final: 0.2673 (tpt) REVERT: D 483 GLU cc_start: 0.5720 (tp30) cc_final: 0.5322 (pm20) REVERT: D 535 TYR cc_start: 0.1137 (t80) cc_final: -0.0620 (p90) REVERT: D 579 MET cc_start: -0.0249 (OUTLIER) cc_final: -0.0594 (mtt) REVERT: E 57 GLU cc_start: 0.2851 (OUTLIER) cc_final: 0.1938 (tp30) REVERT: E 62 MET cc_start: 0.3376 (ttp) cc_final: 0.2842 (tpt) REVERT: E 144 LEU cc_start: 0.0095 (tm) cc_final: -0.0709 (pp) REVERT: E 246 ARG cc_start: 0.1230 (ttp-110) cc_final: 0.0536 (tmm-80) REVERT: E 249 MET cc_start: 0.2479 (ttm) cc_final: 0.2056 (tpp) REVERT: E 271 TRP cc_start: 0.1112 (OUTLIER) cc_final: 0.0895 (m-90) REVERT: E 323 MET cc_start: 0.1470 (tpp) cc_final: 0.0924 (tpp) REVERT: E 328 TRP cc_start: 0.4217 (m100) cc_final: 0.3519 (t-100) REVERT: E 332 MET cc_start: 0.3242 (ptm) cc_final: 0.2664 (ptm) REVERT: E 482 ARG cc_start: 0.4661 (ptt90) cc_final: 0.3864 (mtt180) REVERT: E 546 ASN cc_start: 0.2574 (m110) cc_final: 0.1830 (t0) outliers start: 75 outliers final: 42 residues processed: 229 average time/residue: 1.2636 time to fit residues: 363.9550 Evaluate side-chains 204 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 377 optimal weight: 0.8980 chunk 397 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 386 optimal weight: 10.0000 chunk 396 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 303 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 349 optimal weight: 20.0000 chunk 365 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36012 Z= 0.219 Angle : 0.566 13.076 48965 Z= 0.286 Chirality : 0.044 0.251 5588 Planarity : 0.004 0.047 6257 Dihedral : 5.522 59.687 5942 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.85 % Allowed : 15.62 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4278 helix: 1.53 (0.13), residues: 1462 sheet: 0.30 (0.18), residues: 715 loop : -0.41 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 353 HIS 0.006 0.001 HIS D 239 PHE 0.021 0.001 PHE B 238 TYR 0.021 0.001 TYR A 170 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 162 time to evaluate : 3.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.6251 (p0) cc_final: 0.5913 (m-40) REVERT: A 177 MET cc_start: 0.6092 (pmm) cc_final: 0.4872 (ppp) REVERT: A 740 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7317 (ttp) REVERT: A 780 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: B 740 MET cc_start: 0.8376 (ttt) cc_final: 0.8135 (ttm) REVERT: C 200 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7617 (t80) REVERT: D 45 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6770 (pp) REVERT: D 298 MET cc_start: 0.2651 (mmm) cc_final: 0.2117 (ptt) REVERT: D 313 LYS cc_start: 0.2268 (OUTLIER) cc_final: 0.1762 (ptmt) REVERT: D 408 MET cc_start: 0.3700 (mmp) cc_final: 0.2534 (tpt) REVERT: D 483 GLU cc_start: 0.5708 (tp30) cc_final: 0.5299 (pt0) REVERT: D 535 TYR cc_start: 0.1297 (t80) cc_final: -0.0466 (p90) REVERT: D 579 MET cc_start: -0.0289 (OUTLIER) cc_final: -0.0606 (mtt) REVERT: E 20 LEU cc_start: 0.4203 (tt) cc_final: 0.3880 (mm) REVERT: E 22 GLU cc_start: 0.2309 (tt0) cc_final: 0.1857 (mm-30) REVERT: E 57 GLU cc_start: 0.2942 (OUTLIER) cc_final: 0.2054 (tp30) REVERT: E 62 MET cc_start: 0.3234 (ttp) cc_final: 0.2701 (tpt) REVERT: E 144 LEU cc_start: 0.0129 (tm) cc_final: -0.0665 (pp) REVERT: E 165 TRP cc_start: 0.0434 (OUTLIER) cc_final: -0.0143 (p-90) REVERT: E 246 ARG cc_start: 0.1252 (ttp-110) cc_final: 0.0542 (tmm-80) REVERT: E 249 MET cc_start: 0.2452 (ttm) cc_final: 0.2034 (tpp) REVERT: E 271 TRP cc_start: 0.1109 (OUTLIER) cc_final: 0.0907 (m-90) REVERT: E 298 MET cc_start: 0.1566 (tpp) cc_final: 0.0170 (tmm) REVERT: E 315 PHE cc_start: 0.1170 (OUTLIER) cc_final: 0.0471 (m-80) REVERT: E 323 MET cc_start: 0.1393 (tpp) cc_final: 0.0958 (tpp) REVERT: E 328 TRP cc_start: 0.4427 (m100) cc_final: 0.3512 (t-100) REVERT: E 332 MET cc_start: 0.3167 (ptm) cc_final: 0.2570 (ptm) REVERT: E 366 MET cc_start: -0.0348 (tpt) cc_final: -0.1319 (tmm) REVERT: E 482 ARG cc_start: 0.4850 (ptt90) cc_final: 0.3978 (mtt180) REVERT: E 546 ASN cc_start: 0.2587 (m110) cc_final: 0.1854 (t0) REVERT: E 564 GLU cc_start: 0.4454 (mp0) cc_final: 0.3856 (mt-10) outliers start: 70 outliers final: 44 residues processed: 218 average time/residue: 1.2335 time to fit residues: 336.3610 Evaluate side-chains 206 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 165 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 271 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 384 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 408 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 394 optimal weight: 40.0000 chunk 341 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 263 optimal weight: 4.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.092 36012 Z= 0.727 Angle : 0.774 14.047 48965 Z= 0.395 Chirality : 0.055 0.336 5588 Planarity : 0.005 0.055 6257 Dihedral : 6.476 55.352 5942 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.79 % Allowed : 15.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 4278 helix: 0.98 (0.13), residues: 1453 sheet: -0.06 (0.17), residues: 772 loop : -0.71 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 436 HIS 0.011 0.002 HIS C 954 PHE 0.029 0.003 PHE B 175 TYR 0.033 0.003 TYR A 279 ARG 0.009 0.001 ARG C1000 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8556 Ramachandran restraints generated. 4278 Oldfield, 0 Emsley, 4278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 155 time to evaluate : 4.144 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 52 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 125 ASN cc_start: 0.6179 (p0) cc_final: 0.5688 (m-40) REVERT: A 365 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: A 394 ASN cc_start: 0.5524 (t0) cc_final: 0.5308 (t0) REVERT: A 740 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7403 (ttp) REVERT: A 780 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: B 740 MET cc_start: 0.8459 (ttt) cc_final: 0.8217 (ttm) REVERT: C 200 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7509 (t80) REVERT: C 1010 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: C 1029 MET cc_start: 0.9299 (tpp) cc_final: 0.8968 (tpp) REVERT: D 298 MET cc_start: 0.2592 (mmm) cc_final: 0.2019 (ptt) REVERT: D 313 LYS cc_start: 0.1897 (OUTLIER) cc_final: 0.1320 (ptpt) REVERT: D 387 ARG cc_start: 0.5695 (tmm160) cc_final: 0.5355 (tpm170) REVERT: D 483 GLU cc_start: 0.5751 (tp30) cc_final: 0.5320 (pt0) REVERT: D 494 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5201 (t0) REVERT: D 579 MET cc_start: -0.0409 (OUTLIER) cc_final: -0.0756 (mtt) REVERT: E 22 GLU cc_start: 0.2492 (tt0) cc_final: 0.1742 (mm-30) REVERT: E 57 GLU cc_start: 0.2843 (OUTLIER) cc_final: 0.2515 (pt0) REVERT: E 62 MET cc_start: 0.3390 (ttp) cc_final: 0.2846 (tpt) REVERT: E 128 SER cc_start: 0.1769 (OUTLIER) cc_final: 0.1565 (m) REVERT: E 144 LEU cc_start: 0.0667 (tm) cc_final: -0.0428 (pp) REVERT: E 165 TRP cc_start: 0.0404 (OUTLIER) cc_final: -0.0252 (p-90) REVERT: E 246 ARG cc_start: 0.1262 (ttp-110) cc_final: 0.0875 (tpt170) REVERT: E 249 MET cc_start: 0.2273 (ttm) cc_final: 0.1431 (tpp) REVERT: E 298 MET cc_start: 0.1252 (tpp) cc_final: -0.0097 (tmm) REVERT: E 315 PHE cc_start: 0.1332 (OUTLIER) cc_final: 0.0591 (m-80) REVERT: E 323 MET cc_start: 0.1443 (tpp) cc_final: 0.1125 (tpp) REVERT: E 328 TRP cc_start: 0.4358 (m100) cc_final: 0.3829 (t-100) REVERT: E 332 MET cc_start: 0.2860 (ptm) cc_final: 0.2460 (ptm) REVERT: E 482 ARG cc_start: 0.4530 (ptt90) cc_final: 0.3723 (mtt180) REVERT: E 534 LYS cc_start: 0.2731 (tppt) cc_final: 0.2502 (mppt) REVERT: E 546 ASN cc_start: 0.2398 (m110) cc_final: 0.1678 (t0) outliers start: 68 outliers final: 44 residues processed: 214 average time/residue: 1.1773 time to fit residues: 316.8691 Evaluate side-chains 205 residues out of total 3790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 149 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 313 LYS Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 165 TRP Chi-restraints excluded: chain E residue 203 TRP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 430 random chunks: chunk 209 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 363 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 341 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 613 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.173747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.098965 restraints weight = 72722.060| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.14 r_work: 0.3170 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 36012 Z= 0.362 Angle : 0.636 13.726 48965 Z= 0.322 Chirality : 0.046 0.265 5588 Planarity : 0.004 0.052 6257 Dihedral : 6.121 55.966 5942 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.82 % Allowed : 15.83 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4278 helix: 1.21 (0.13), residues: 1452 sheet: 0.02 (0.18), residues: 745 loop : -0.60 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 271 HIS 0.005 0.001 HIS D 239 PHE 0.025 0.002 PHE A 855 TYR 0.029 0.002 TYR E 158 ARG 0.005 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12383.82 seconds wall clock time: 221 minutes 28.87 seconds (13288.87 seconds total)