Starting phenix.real_space_refine on Fri Jul 26 13:43:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wlo_37626/07_2024/8wlo_37626_neut.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2984 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 142 5.16 5 C 19396 2.51 5 N 5008 2.21 5 O 5917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "E GLU 58": "OE1" <-> "OE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.57s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30464 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8290 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8292 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 58, 'TRANS': 1002} Chain breaks: 6 Chain: "C" Number of atoms: 8322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8322 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 58, 'TRANS': 1006} Chain breaks: 6 Chain: "E" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4873 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 6 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: "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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.66, per 1000 atoms: 0.58 Number of scatterers: 30464 At special positions: 0 Unit cell: (140.25, 147.05, 249.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 142 16.00 O 5917 8.00 N 5008 7.00 C 19396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, 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=2.04 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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 D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG 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-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 801 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 282 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 17 " " NAG D 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " Time building additional restraints: 11.68 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 374 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 378 " 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7110 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 31.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.045A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.544A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.668A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.544A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.554A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.892A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.562A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.623A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.504A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.169A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.689A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.824A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.826A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.289A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.359A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 371 removed outlier: 4.011A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.843A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.676A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.580A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.537A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.517A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.229A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.848A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.091A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.908A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.155A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.838A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.575A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.654A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 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: 3.694A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.556A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.508A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.625A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.319A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.943A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.857A pdb=" N GLN E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 28 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP E 39 " --> pdb=" O HIS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 81 removed outlier: 3.515A pdb=" N VAL E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.863A pdb=" N GLN E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 4.189A pdb=" N ALA E 108 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 109' Processing helix chain 'E' and resid 110 through 127 removed outlier: 3.532A pdb=" N ILE E 127 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 131 removed outlier: 3.713A pdb=" N GLY E 131 " --> pdb=" O TYR E 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 128 through 131' Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.542A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 194 removed outlier: 3.743A pdb=" N GLU E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 4.200A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (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 220 through 249 removed outlier: 3.779A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.788A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.591A pdb=" N PHE E 308 " --> pdb=" O THR E 304 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.013A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.585A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.901A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 412 " --> pdb=" O MET E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 446 removed outlier: 3.873A pdb=" N ASN E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.659A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.674A pdb=" N TRP E 478 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU E 483 " --> pdb=" O GLU E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.170A pdb=" N ALA E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 508' Processing helix chain 'E' and resid 512 through 534 removed outlier: 4.133A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.623A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG E 553 " --> pdb=" O ASP E 549 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 557 " --> pdb=" O ARG E 553 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU E 560 " --> pdb=" O GLN E 556 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.717A pdb=" N ILE E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'E' and resid 597 through 601 removed outlier: 3.722A pdb=" N ASN E 601 " --> pdb=" O GLN E 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.732A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.715A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.914A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.515A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.105A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.119A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.871A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.962A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.775A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.415A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.691A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.064A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.979A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.056A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.805A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.058A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.095A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.770A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.073A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.073A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.784A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.515A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 117 removed outlier: 3.551A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 141 removed outlier: 4.292A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.603A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 202 through 205 removed outlier: 7.056A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.102A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.693A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.663A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.547A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 712 removed outlier: 3.731A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 728 removed outlier: 6.131A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.727A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.397A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.821A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 1161 hydrogen bonds defined for protein. 3207 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: 11.84 Time building geometry restraints manager: 12.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9739 1.34 - 1.46: 7560 1.46 - 1.58: 13686 1.58 - 1.70: 2 1.70 - 1.82: 189 Bond restraints: 31176 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 1.302 0.201 3.40e-02 8.65e+02 3.50e+01 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.673 -0.181 5.00e-02 4.00e+02 1.32e+01 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 31171 not shown) Histogram of bond angle deviations from ideal: 89.79 - 98.66: 5 98.66 - 107.52: 1176 107.52 - 116.39: 20143 116.39 - 125.25: 20659 125.25 - 134.12: 448 Bond angle restraints: 42431 Sorted by residual: angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 94.20 17.80 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 89.79 13.41 1.50e+00 4.44e-01 7.99e+01 angle pdb=" CA PRO B 25 " pdb=" N PRO B 25 " pdb=" CD PRO B 25 " ideal model delta sigma weight residual 112.00 101.68 10.32 1.40e+00 5.10e-01 5.43e+01 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 94.41 10.09 1.90e+00 2.77e-01 2.82e+01 angle pdb=" CB MET E 462 " pdb=" CG MET E 462 " pdb=" SD MET E 462 " ideal model delta sigma weight residual 112.70 124.77 -12.07 3.00e+00 1.11e-01 1.62e+01 ... (remaining 42426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.74: 17768 24.74 - 49.49: 1241 49.49 - 74.23: 166 74.23 - 98.97: 44 98.97 - 123.72: 17 Dihedral angle restraints: 19236 sinusoidal: 8198 harmonic: 11038 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -30.61 -55.39 1 1.00e+01 1.00e-02 4.15e+01 ... (remaining 19233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4864 0.130 - 0.259: 35 0.259 - 0.389: 3 0.389 - 0.518: 0 0.518 - 0.648: 3 Chirality restraints: 4905 Sorted by residual: chirality pdb=" C1 NAG B1312 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1312 " pdb=" O5 NAG B1312 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.28e+00 ... (remaining 4902 not shown) Planarity restraints: 5471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " 0.115 5.00e-02 4.00e+02 1.57e-01 3.94e+01 pdb=" N PRO B 384 " -0.270 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 82 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.058 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO B 25 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.045 5.00e-02 4.00e+02 ... (remaining 5468 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 433 2.65 - 3.21: 27595 3.21 - 3.77: 45288 3.77 - 4.34: 61945 4.34 - 4.90: 102848 Nonbonded interactions: 238109 Sorted by model distance: nonbonded pdb=" CB HIS E 378 " pdb="ZN ZN E 701 " model vdw 2.086 2.104 nonbonded pdb=" N GLU A 309 " pdb=" OE1 GLU A 309 " model vdw 2.174 2.520 nonbonded pdb=" O THR C 124 " pdb=" OG1 THR C 124 " model vdw 2.179 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR E 128 " pdb=" O LEU E 503 " model vdw 2.191 2.440 ... (remaining 238104 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' and (resid 14 through 257 or resid 262 through 1147 or resid 1301 thr \ ough 1306)) selection = (chain 'B' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 141 or resid 154 through 176 or resid 188 throu \ gh 257 or resid 262 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = 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' } 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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 84.090 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 31176 Z= 0.274 Angle : 0.664 17.797 42431 Z= 0.334 Chirality : 0.048 0.648 4905 Planarity : 0.005 0.157 5434 Dihedral : 16.704 123.718 11997 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.60 % Allowed : 25.04 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3740 helix: 1.85 (0.18), residues: 957 sheet: 0.42 (0.20), residues: 670 loop : -0.83 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 436 HIS 0.004 0.000 HIS C 245 PHE 0.038 0.001 PHE C 168 TYR 0.039 0.001 TYR B 505 ARG 0.009 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5208 (mmt) cc_final: 0.4934 (tpt) REVERT: B 853 GLN cc_start: 0.5084 (OUTLIER) cc_final: 0.3808 (mt0) REVERT: E 249 MET cc_start: -0.0369 (mmm) cc_final: -0.1187 (mmt) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 1.1495 time to fit residues: 163.5721 Evaluate side-chains 78 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain E residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 342 optimal weight: 50.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 334 ASN A 414 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 690 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 953 ASN A 965 GLN A1010 GLN B 14 GLN B 218 GLN B 354 ASN B 422 ASN B 439 ASN B 493 GLN B 501 ASN B 544 ASN B 613 GLN B 628 GLN B 658 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN B 978 ASN B1135 ASN C 23 GLN C 122 ASN C 137 ASN C 196 ASN C 314 GLN C 321 GLN C 422 ASN C 448 ASN C 501 ASN C 658 ASN C 675 GLN C 901 GLN ** E 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN E 102 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS E 475 GLN E 493 HIS E 524 GLN E 531 GLN ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 31176 Z= 0.443 Angle : 0.679 9.481 42431 Z= 0.340 Chirality : 0.050 0.579 4905 Planarity : 0.005 0.067 5434 Dihedral : 9.606 103.431 5107 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.31 % Allowed : 20.64 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: -0.04 (0.14), residues: 3740 helix: 1.53 (0.17), residues: 1004 sheet: 0.28 (0.19), residues: 726 loop : -0.96 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 633 HIS 0.004 0.001 HIS E 373 PHE 0.021 0.002 PHE C 800 TYR 0.018 0.002 TYR A1067 ARG 0.006 0.001 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 71 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: B 153 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4870 (tpt) REVERT: B 335 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8010 (tm) REVERT: B 591 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9193 (p) REVERT: B 853 GLN cc_start: 0.5107 (OUTLIER) cc_final: 0.4112 (mt0) REVERT: E 249 MET cc_start: -0.0402 (mmm) cc_final: -0.0742 (mmt) REVERT: E 579 MET cc_start: 0.0486 (mmp) cc_final: -0.0326 (tpt) outliers start: 143 outliers final: 45 residues processed: 201 average time/residue: 0.9295 time to fit residues: 242.0018 Evaluate side-chains 111 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 61 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 261 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 342 optimal weight: 50.0000 chunk 370 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 340 optimal weight: 50.0000 chunk 116 optimal weight: 0.9980 chunk 275 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 498 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31176 Z= 0.182 Angle : 0.572 9.597 42431 Z= 0.283 Chirality : 0.046 0.511 4905 Planarity : 0.004 0.053 5434 Dihedral : 8.287 100.119 5102 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.47 % Allowed : 21.63 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3740 helix: 1.64 (0.17), residues: 1015 sheet: 0.41 (0.19), residues: 706 loop : -0.85 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.010 0.001 HIS E 374 PHE 0.025 0.001 PHE C 168 TYR 0.014 0.001 TYR B 369 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 67 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: A 645 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8834 (p) REVERT: A 995 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8359 (ptp-170) REVERT: A 1043 CYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8754 (m) REVERT: B 14 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: B 335 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8034 (tm) REVERT: B 591 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.9159 (p) REVERT: C 153 MET cc_start: 0.4543 (pmt) cc_final: 0.4114 (pmt) REVERT: E 154 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6573 (p0) REVERT: E 249 MET cc_start: -0.0217 (mmm) cc_final: -0.0774 (mmp) outliers start: 82 outliers final: 31 residues processed: 142 average time/residue: 1.0035 time to fit residues: 180.8598 Evaluate side-chains 102 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 63 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 14 GLN Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 40.0000 chunk 257 optimal weight: 0.0570 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 163 optimal weight: 0.0870 chunk 230 optimal weight: 7.9990 chunk 344 optimal weight: 6.9990 chunk 364 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 overall best weight: 1.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31176 Z= 0.229 Angle : 0.560 9.807 42431 Z= 0.276 Chirality : 0.045 0.431 4905 Planarity : 0.004 0.051 5434 Dihedral : 7.728 96.310 5099 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.04 % Allowed : 20.61 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3740 helix: 1.75 (0.17), residues: 1021 sheet: 0.41 (0.19), residues: 707 loop : -0.80 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.006 0.001 HIS E 374 PHE 0.025 0.001 PHE A 456 TYR 0.014 0.001 TYR C1067 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 64 time to evaluate : 3.548 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 318 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8938 (p90) REVERT: A 583 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: A 586 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: A 645 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8817 (p) REVERT: B 34 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8001 (mtp85) REVERT: B 335 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8032 (tm) REVERT: B 825 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (mmmt) REVERT: C 153 MET cc_start: 0.4560 (pmt) cc_final: 0.4127 (pmt) REVERT: E 249 MET cc_start: -0.0280 (mmm) cc_final: -0.0738 (mmp) outliers start: 101 outliers final: 47 residues processed: 155 average time/residue: 1.0903 time to fit residues: 215.6078 Evaluate side-chains 117 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 63 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31176 Z= 0.201 Angle : 0.547 10.143 42431 Z= 0.268 Chirality : 0.045 0.406 4905 Planarity : 0.004 0.051 5434 Dihedral : 7.318 93.803 5099 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.07 % Allowed : 20.73 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3740 helix: 1.83 (0.17), residues: 1023 sheet: 0.48 (0.19), residues: 703 loop : -0.77 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 633 HIS 0.006 0.001 HIS E 374 PHE 0.015 0.001 PHE C 800 TYR 0.014 0.001 TYR C 265 ARG 0.009 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 64 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8879 (p90) REVERT: A 583 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: A 586 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: A 645 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 1043 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8762 (m) REVERT: B 335 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8069 (tm) REVERT: B 591 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.9162 (p) REVERT: C 153 MET cc_start: 0.4471 (pmt) cc_final: 0.4022 (pmt) REVERT: E 154 ASN cc_start: 0.6896 (OUTLIER) cc_final: 0.6630 (p0) REVERT: E 249 MET cc_start: -0.0209 (mmm) cc_final: -0.0440 (mmp) outliers start: 102 outliers final: 50 residues processed: 159 average time/residue: 0.9232 time to fit residues: 190.1026 Evaluate side-chains 120 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 62 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 1.9990 chunk 328 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 213 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 364 optimal weight: 40.0000 chunk 302 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 0.6980 chunk 191 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS E 277 ASN ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31176 Z= 0.233 Angle : 0.553 10.445 42431 Z= 0.272 Chirality : 0.045 0.396 4905 Planarity : 0.004 0.054 5434 Dihedral : 7.110 90.961 5099 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.83 % Allowed : 20.70 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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 (0.14), residues: 3740 helix: 1.89 (0.17), residues: 1024 sheet: 0.46 (0.19), residues: 703 loop : -0.77 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.017 0.001 PHE B 342 TYR 0.015 0.001 TYR C1067 ARG 0.005 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 65 time to evaluate : 3.427 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 318 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8863 (p90) REVERT: A 583 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: A 586 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8317 (m-30) REVERT: A 645 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8841 (p) REVERT: B 34 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: B 335 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8087 (tm) REVERT: B 591 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9166 (p) REVERT: B 825 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (mmmt) REVERT: C 153 MET cc_start: 0.4418 (OUTLIER) cc_final: 0.3936 (pmt) REVERT: E 154 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6609 (p0) REVERT: E 249 MET cc_start: -0.0102 (mmm) cc_final: -0.0617 (mmp) outliers start: 94 outliers final: 57 residues processed: 150 average time/residue: 1.0395 time to fit residues: 197.7854 Evaluate side-chains 129 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 62 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 40.0000 chunk 41 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 chunk 206 optimal weight: 0.7980 chunk 307 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 363 optimal weight: 40.0000 chunk 227 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31176 Z= 0.270 Angle : 0.565 10.859 42431 Z= 0.279 Chirality : 0.045 0.400 4905 Planarity : 0.004 0.054 5434 Dihedral : 6.954 87.064 5098 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.16 % Allowed : 20.64 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.14), residues: 3740 helix: 1.91 (0.17), residues: 1023 sheet: 0.39 (0.19), residues: 715 loop : -0.80 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 633 HIS 0.006 0.001 HIS E 374 PHE 0.017 0.001 PHE C 800 TYR 0.033 0.001 TYR B 505 ARG 0.004 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 62 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8639 (m) REVERT: A 318 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8820 (p90) REVERT: A 583 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: A 586 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 645 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 1043 CYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8760 (m) REVERT: B 34 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8150 (mtp85) REVERT: B 215 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8686 (OUTLIER) REVERT: B 335 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8028 (tm) REVERT: B 591 SER cc_start: 0.9386 (OUTLIER) cc_final: 0.9167 (p) REVERT: B 825 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8676 (mmmt) REVERT: C 153 MET cc_start: 0.4408 (OUTLIER) cc_final: 0.3899 (pmt) REVERT: E 154 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6599 (p0) REVERT: E 249 MET cc_start: -0.0053 (mmm) cc_final: -0.0558 (mmp) outliers start: 105 outliers final: 60 residues processed: 159 average time/residue: 0.9510 time to fit residues: 193.6743 Evaluate side-chains 134 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 62 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 231 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 285 optimal weight: 0.0770 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31176 Z= 0.217 Angle : 0.553 11.232 42431 Z= 0.272 Chirality : 0.045 0.475 4905 Planarity : 0.004 0.054 5434 Dihedral : 6.734 82.880 5098 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.71 % Allowed : 20.79 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.35 (0.14), residues: 3740 helix: 1.95 (0.17), residues: 1022 sheet: 0.46 (0.19), residues: 705 loop : -0.76 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.019 0.001 PHE C 168 TYR 0.029 0.001 TYR B 505 ARG 0.003 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 64 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 318 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8753 (p90) REVERT: A 583 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: A 586 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: A 645 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 1043 CYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8753 (m) REVERT: B 34 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8148 (mtp85) REVERT: B 335 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8021 (tm) REVERT: B 591 SER cc_start: 0.9380 (OUTLIER) cc_final: 0.9159 (p) REVERT: B 825 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8670 (mmmt) REVERT: C 153 MET cc_start: 0.4464 (OUTLIER) cc_final: 0.3939 (pmt) REVERT: E 154 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.6591 (p0) REVERT: E 163 TRP cc_start: 0.6921 (OUTLIER) cc_final: 0.5667 (p-90) REVERT: E 249 MET cc_start: -0.0005 (mmm) cc_final: -0.0498 (mmp) REVERT: E 579 MET cc_start: -0.0017 (tpp) cc_final: -0.0249 (tpp) outliers start: 90 outliers final: 59 residues processed: 151 average time/residue: 0.9920 time to fit residues: 192.5723 Evaluate side-chains 136 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 64 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 7.9990 chunk 348 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 338 optimal weight: 30.0000 chunk 203 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 305 optimal weight: 2.9990 chunk 320 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31176 Z= 0.183 Angle : 0.554 11.838 42431 Z= 0.272 Chirality : 0.045 0.540 4905 Planarity : 0.004 0.054 5434 Dihedral : 6.505 78.585 5098 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.47 % Allowed : 21.09 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3740 helix: 2.00 (0.17), residues: 1020 sheet: 0.49 (0.19), residues: 706 loop : -0.73 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.004 0.001 HIS E 374 PHE 0.015 0.001 PHE B 456 TYR 0.028 0.001 TYR B 505 ARG 0.003 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 67 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8824 (p90) REVERT: A 583 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8276 (pm20) REVERT: A 586 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: A 645 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8859 (p) REVERT: A 1043 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8759 (m) REVERT: B 34 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8142 (mtp85) REVERT: B 215 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8650 (p0) REVERT: B 335 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8034 (tm) REVERT: B 402 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7016 (tt) REVERT: B 591 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.9161 (p) REVERT: B 825 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8669 (mmmt) REVERT: C 153 MET cc_start: 0.4528 (pmt) cc_final: 0.4026 (pmt) REVERT: E 154 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6603 (p0) REVERT: E 163 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.5609 (p-90) REVERT: E 249 MET cc_start: -0.0029 (mmm) cc_final: -0.0508 (mmp) REVERT: E 579 MET cc_start: 0.0152 (tpp) cc_final: -0.0141 (tpp) outliers start: 82 outliers final: 58 residues processed: 146 average time/residue: 0.9884 time to fit residues: 184.9713 Evaluate side-chains 133 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 62 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 10.0000 chunk 358 optimal weight: 40.0000 chunk 218 optimal weight: 9.9990 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 375 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN E 61 GLN ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 31176 Z= 0.431 Angle : 0.642 15.281 42431 Z= 0.320 Chirality : 0.048 0.632 4905 Planarity : 0.004 0.054 5434 Dihedral : 6.765 76.680 5097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.41 % Allowed : 21.15 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.14), residues: 3740 helix: 1.84 (0.17), residues: 1041 sheet: 0.38 (0.19), residues: 709 loop : -0.88 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 633 HIS 0.005 0.001 HIS E 374 PHE 0.022 0.002 PHE C 800 TYR 0.027 0.001 TYR B 505 ARG 0.004 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7480 Ramachandran restraints generated. 3740 Oldfield, 0 Emsley, 3740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 61 time to evaluate : 3.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8621 (p90) REVERT: A 583 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: A 586 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: A 645 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8833 (p) REVERT: B 34 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8340 (mtp85) REVERT: B 335 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7921 (tm) REVERT: B 591 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9137 (p) REVERT: B 825 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8747 (mmmt) REVERT: C 153 MET cc_start: 0.4413 (pmt) cc_final: 0.3878 (pmt) REVERT: C 787 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: E 152 MET cc_start: 0.1317 (ptp) cc_final: 0.0877 (pmm) REVERT: E 163 TRP cc_start: 0.6864 (OUTLIER) cc_final: 0.5366 (p-90) REVERT: E 249 MET cc_start: -0.0130 (mmm) cc_final: -0.0592 (mmp) REVERT: E 579 MET cc_start: 0.0342 (tpp) cc_final: 0.0053 (tpp) outliers start: 80 outliers final: 60 residues processed: 138 average time/residue: 1.0492 time to fit residues: 182.1398 Evaluate side-chains 131 residues out of total 3320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 61 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain E residue 61 GLN Chi-restraints excluded: chain E residue 163 TRP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 438 PHE Chi-restraints excluded: chain E residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 0.9990 chunk 318 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 299 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS E 61 GLN E 522 GLN ** E 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.100949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059158 restraints weight = 103805.896| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.37 r_work: 0.2792 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31176 Z= 0.187 Angle : 0.573 14.798 42431 Z= 0.281 Chirality : 0.045 0.542 4905 Planarity : 0.004 0.055 5434 Dihedral : 6.413 75.164 5097 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 21.60 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % 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: 0.34 (0.14), residues: 3740 helix: 1.96 (0.17), residues: 1019 sheet: 0.47 (0.19), residues: 701 loop : -0.79 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.004 0.001 HIS E 374 PHE 0.019 0.001 PHE A 79 TYR 0.027 0.001 TYR B 505 ARG 0.004 0.000 ARG A 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8482.61 seconds wall clock time: 150 minutes 56.38 seconds (9056.38 seconds total)