Starting phenix.real_space_refine on Mon Feb 19 19:30:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1b_14237/02_2024/7r1b_14237.pdb" } resolution = 2.8 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= 0.004 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16269 2.51 5 N 4209 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25554 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8297 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 53, 'TRANS': 1007} Chain breaks: 5 Chain: "B" Number of atoms: 8352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8352 Classifications: {'peptide': 1068} Link IDs: {'PTRANS': 54, 'TRANS': 1013} Chain breaks: 5 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8317 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 54, 'TRANS': 1009} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 12.74, per 1000 atoms: 0.50 Number of scatterers: 25554 At special positions: 0 Unit cell: (157.388, 153.076, 198.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4962 8.00 N 4209 7.00 C 16269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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=2.04 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 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1134 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 331 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN C1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 9.00 Conformation dependent library (CDL) restraints added in 4.4 seconds 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 47 sheets defined 23.5% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.943A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.128A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.386A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.746A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.543A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.847A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.749A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.350A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.797A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.125A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.262A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (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 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.831A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.965A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.076A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.012A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.530A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.017A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.573A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 4.216A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.569A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.676A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.155A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.824A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.808A 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.275A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.975A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.627A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.551A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.957A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.888A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 106 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 119 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 319 removed outlier: 5.333A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.366A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.971A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.610A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.215A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.785A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.682A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.544A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.068A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.889A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.889A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.332A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.652A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.909A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.396A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.711A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.973A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.743A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AE1, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.049A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.565A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.573A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.743A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.576A pdb=" N PHE C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.327A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.539A 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 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.695A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.673A 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 1122 980 hydrogen bonds defined for protein. 2739 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: 11.98 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5462 1.33 - 1.45: 6496 1.45 - 1.58: 14031 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 26133 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N VAL A 171 " pdb=" CA VAL A 171 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.14e+01 bond pdb=" N ILE A 235 " pdb=" CA ILE A 235 " ideal model delta sigma weight residual 1.464 1.501 -0.037 1.13e-02 7.83e+03 1.08e+01 bond pdb=" N VAL A 126 " pdb=" CA VAL A 126 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.08e-02 8.57e+03 1.03e+01 bond pdb=" N VAL C 911 " pdb=" CA VAL C 911 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.14e-02 7.69e+03 9.97e+00 ... (remaining 26128 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.82: 780 106.82 - 113.68: 14393 113.68 - 120.54: 9935 120.54 - 127.40: 10248 127.40 - 134.26: 205 Bond angle restraints: 35561 Sorted by residual: angle pdb=" CA ASN A 121 " pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 122.64 117.78 4.86 1.25e+00 6.40e-01 1.51e+01 angle pdb=" N PRO B 600 " pdb=" CA PRO B 600 " pdb=" C PRO B 600 " ideal model delta sigma weight residual 111.41 105.62 5.79 1.50e+00 4.44e-01 1.49e+01 angle pdb=" CA GLY B 601 " pdb=" C GLY B 601 " pdb=" O GLY B 601 " ideal model delta sigma weight residual 121.41 118.05 3.36 8.80e-01 1.29e+00 1.46e+01 angle pdb=" CA THR B 33 " pdb=" C THR B 33 " pdb=" O THR B 33 " ideal model delta sigma weight residual 121.84 117.44 4.40 1.16e+00 7.43e-01 1.44e+01 angle pdb=" N THR B 470 " pdb=" CA THR B 470 " pdb=" C THR B 470 " ideal model delta sigma weight residual 111.28 107.14 4.14 1.09e+00 8.42e-01 1.44e+01 ... (remaining 35556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 14886 17.56 - 35.12: 1030 35.12 - 52.68: 160 52.68 - 70.25: 33 70.25 - 87.81: 15 Dihedral angle restraints: 16124 sinusoidal: 6839 harmonic: 9285 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -145.45 59.45 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 55.86 37.14 1 1.00e+01 1.00e-02 1.95e+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 -49.43 -36.57 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 16121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3879 0.104 - 0.208: 244 0.208 - 0.312: 19 0.312 - 0.416: 0 0.416 - 0.520: 1 Chirality restraints: 4143 Sorted by residual: chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 657 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 4140 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 127 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C VAL B 127 " -0.077 2.00e-02 2.50e+03 pdb=" O VAL B 127 " 0.029 2.00e-02 2.50e+03 pdb=" N ILE B 128 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 617 " -0.019 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C CYS A 617 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS A 617 " -0.023 2.00e-02 2.50e+03 pdb=" N THR A 618 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 603 " -0.001 2.00e-02 2.50e+03 1.69e-02 3.56e+00 pdb=" CG ASN C 603 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN C 603 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 603 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.018 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3042 2.76 - 3.29: 23300 3.29 - 3.83: 39265 3.83 - 4.36: 47674 4.36 - 4.90: 83776 Nonbonded interactions: 197057 Sorted by model distance: nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN A 394 " pdb=" OH TYR B 200 " model vdw 2.239 2.440 nonbonded pdb=" OG SER A 98 " pdb=" O LYS A 182 " model vdw 2.316 2.440 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.323 2.440 ... (remaining 197052 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 675 or resid 690 through 1146 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1146 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 620 or resid 641 through 826 or resid 856 throu \ gh 1146 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.220 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 66.710 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.240 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26133 Z= 0.300 Angle : 0.675 7.543 35561 Z= 0.420 Chirality : 0.054 0.520 4143 Planarity : 0.004 0.044 4562 Dihedral : 12.031 87.807 10026 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.54 % Allowed : 0.90 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3157 helix: 1.85 (0.21), residues: 660 sheet: 0.38 (0.19), residues: 705 loop : -1.27 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 886 HIS 0.004 0.001 HIS A 207 PHE 0.018 0.001 PHE C 490 TYR 0.017 0.001 TYR B 37 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 CYS cc_start: 0.3499 (OUTLIER) cc_final: 0.3208 (m) REVERT: A 188 ASN cc_start: 0.7950 (OUTLIER) cc_final: 0.7477 (p0) REVERT: A 378 LYS cc_start: 0.6900 (mttp) cc_final: 0.6461 (mtpp) REVERT: A 409 GLN cc_start: 0.7806 (mt0) cc_final: 0.7601 (mt0) REVERT: A 455 LEU cc_start: 0.8047 (tt) cc_final: 0.7777 (tm) REVERT: B 99 ASN cc_start: 0.8213 (m-40) cc_final: 0.7464 (t0) REVERT: B 129 LYS cc_start: 0.7383 (mptt) cc_final: 0.7086 (mmtp) REVERT: C 53 ASP cc_start: 0.6657 (t0) cc_final: 0.6383 (t70) REVERT: C 237 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6638 (mtm110) REVERT: C 529 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7904 (mmpt) REVERT: C 697 MET cc_start: 0.8242 (ptm) cc_final: 0.8003 (ptp) REVERT: C 988 GLU cc_start: 0.6507 (tp30) cc_final: 0.6285 (tp30) outliers start: 15 outliers final: 3 residues processed: 267 average time/residue: 1.1773 time to fit residues: 372.3682 Evaluate side-chains 189 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 68 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.2980 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 0.2980 chunk 96 optimal weight: 0.0980 chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 764 ASN A 969 ASN B 122 ASN B 146 HIS B 165 ASN B 218 GLN B 532 ASN C 314 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 26133 Z= 0.161 Angle : 0.533 12.698 35561 Z= 0.276 Chirality : 0.045 0.367 4143 Planarity : 0.004 0.045 4562 Dihedral : 6.233 59.602 4311 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.11 % Allowed : 6.56 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3157 helix: 2.04 (0.21), residues: 676 sheet: 0.54 (0.19), residues: 725 loop : -1.21 (0.13), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.006 0.001 HIS C 207 PHE 0.022 0.001 PHE C 400 TYR 0.020 0.001 TYR A1067 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 193 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7287 (tm-30) REVERT: A 254 SER cc_start: 0.2970 (OUTLIER) cc_final: 0.2039 (p) REVERT: A 378 LYS cc_start: 0.6780 (mttp) cc_final: 0.6288 (mtpp) REVERT: A 409 GLN cc_start: 0.7715 (mt0) cc_final: 0.7394 (mt0) REVERT: A 455 LEU cc_start: 0.8059 (tt) cc_final: 0.7735 (tm) REVERT: A 508 TYR cc_start: 0.7455 (m-80) cc_final: 0.7115 (m-80) REVERT: A 745 ASP cc_start: 0.7328 (p0) cc_final: 0.7059 (p0) REVERT: B 129 LYS cc_start: 0.7534 (mptt) cc_final: 0.7290 (mmmt) REVERT: B 177 MET cc_start: 0.4170 (ttm) cc_final: 0.1853 (pmt) REVERT: B 532 ASN cc_start: 0.7695 (t0) cc_final: 0.7494 (t160) REVERT: B 586 ASP cc_start: 0.7917 (m-30) cc_final: 0.7685 (m-30) REVERT: C 177 MET cc_start: 0.2468 (pmt) cc_final: 0.2139 (pmm) REVERT: C 237 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6326 (mtm110) REVERT: C 529 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7909 (mmpt) REVERT: C 988 GLU cc_start: 0.6477 (tp30) cc_final: 0.6232 (tp30) outliers start: 31 outliers final: 12 residues processed: 212 average time/residue: 1.1116 time to fit residues: 283.4368 Evaluate side-chains 184 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 257 optimal weight: 50.0000 chunk 286 optimal weight: 0.0370 chunk 98 optimal weight: 0.6980 chunk 232 optimal weight: 0.0170 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN C 99 ASN C 234 ASN C 394 ASN C 675 GLN C 919 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26133 Z= 0.194 Angle : 0.529 12.986 35561 Z= 0.274 Chirality : 0.045 0.297 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.907 59.994 4307 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.72 % Allowed : 7.89 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3157 helix: 2.13 (0.21), residues: 664 sheet: 0.55 (0.19), residues: 734 loop : -1.25 (0.13), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 886 HIS 0.005 0.001 HIS C1048 PHE 0.016 0.001 PHE B 392 TYR 0.022 0.001 TYR A1067 ARG 0.004 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 THR cc_start: 0.6420 (OUTLIER) cc_final: 0.5853 (m) REVERT: A 166 CYS cc_start: 0.3060 (OUTLIER) cc_final: 0.2853 (m) REVERT: A 177 MET cc_start: -0.0067 (pmm) cc_final: -0.0369 (ptp) REVERT: A 188 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7817 (p0) REVERT: A 378 LYS cc_start: 0.6864 (mttp) cc_final: 0.6338 (mtpp) REVERT: A 409 GLN cc_start: 0.7733 (mt0) cc_final: 0.7462 (mt0) REVERT: A 455 LEU cc_start: 0.8065 (tt) cc_final: 0.7706 (tm) REVERT: A 508 TYR cc_start: 0.7508 (m-80) cc_final: 0.7107 (m-80) REVERT: A 613 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: A 745 ASP cc_start: 0.7395 (p0) cc_final: 0.7037 (p0) REVERT: A 916 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8497 (tp) REVERT: B 177 MET cc_start: 0.3928 (ttm) cc_final: 0.1765 (pmt) REVERT: B 586 ASP cc_start: 0.7743 (m-30) cc_final: 0.7500 (m-30) REVERT: C 80 ASP cc_start: 0.6362 (p0) cc_final: 0.5031 (m-30) REVERT: C 153 MET cc_start: 0.7112 (pmm) cc_final: 0.6536 (pp-130) REVERT: C 237 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6407 (mtm110) REVERT: C 529 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7910 (mmpt) REVERT: C 988 GLU cc_start: 0.6531 (tp30) cc_final: 0.6327 (tp30) outliers start: 48 outliers final: 16 residues processed: 212 average time/residue: 1.0528 time to fit residues: 271.9225 Evaluate side-chains 193 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 290 optimal weight: 0.0060 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 50.0000 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN B 532 ASN C 146 HIS C 394 ASN C 675 GLN C 901 GLN C1002 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 26133 Z= 0.383 Angle : 0.644 11.135 35561 Z= 0.335 Chirality : 0.050 0.287 4143 Planarity : 0.005 0.054 4562 Dihedral : 6.168 59.294 4307 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.58 % Allowed : 8.57 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3157 helix: 1.58 (0.21), residues: 656 sheet: 0.37 (0.19), residues: 751 loop : -1.49 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.008 0.002 HIS C1048 PHE 0.023 0.002 PHE C 168 TYR 0.028 0.002 TYR A1067 ARG 0.009 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 178 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7741 (p0) REVERT: A 378 LYS cc_start: 0.6813 (mttp) cc_final: 0.6293 (mtpp) REVERT: A 409 GLN cc_start: 0.7739 (mt0) cc_final: 0.7471 (mt0) REVERT: A 455 LEU cc_start: 0.8096 (tt) cc_final: 0.7761 (tm) REVERT: A 508 TYR cc_start: 0.7520 (m-80) cc_final: 0.7184 (m-80) REVERT: A 745 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7012 (p0) REVERT: A 916 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8620 (tp) REVERT: B 32 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: B 117 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.6944 (tt) REVERT: B 129 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7537 (mmmt) REVERT: B 177 MET cc_start: 0.4105 (ttm) cc_final: 0.1972 (pmt) REVERT: B 586 ASP cc_start: 0.7768 (m-30) cc_final: 0.7476 (m-30) REVERT: C 153 MET cc_start: 0.7078 (pmm) cc_final: 0.6564 (pp-130) REVERT: C 169 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: C 237 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6435 (mtm110) REVERT: C 529 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7910 (mmpt) REVERT: C 988 GLU cc_start: 0.6718 (tp30) cc_final: 0.6391 (tp30) REVERT: C 1002 GLN cc_start: 0.7731 (tt0) cc_final: 0.7502 (tt0) outliers start: 72 outliers final: 31 residues processed: 225 average time/residue: 1.0391 time to fit residues: 283.5529 Evaluate side-chains 208 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 7.9990 chunk 174 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 212 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 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 564 GLN A 969 ASN A1010 GLN B 532 ASN C 394 ASN C 675 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26133 Z= 0.282 Angle : 0.581 15.023 35561 Z= 0.302 Chirality : 0.047 0.296 4143 Planarity : 0.004 0.052 4562 Dihedral : 5.992 59.437 4307 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.47 % Allowed : 9.82 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3157 helix: 1.58 (0.21), residues: 659 sheet: 0.43 (0.19), residues: 740 loop : -1.51 (0.13), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.015 0.002 PHE A1121 TYR 0.022 0.001 TYR A1067 ARG 0.009 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7781 (p0) REVERT: A 378 LYS cc_start: 0.6890 (mttp) cc_final: 0.6332 (mtpp) REVERT: A 390 LEU cc_start: 0.8006 (mt) cc_final: 0.7742 (mt) REVERT: A 455 LEU cc_start: 0.8058 (tt) cc_final: 0.7729 (tm) REVERT: A 508 TYR cc_start: 0.7392 (m-80) cc_final: 0.7114 (m-80) REVERT: A 745 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6993 (p0) REVERT: A 916 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8582 (tp) REVERT: B 129 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7588 (mmmt) REVERT: B 177 MET cc_start: 0.4105 (ttm) cc_final: 0.1979 (pmt) REVERT: B 314 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8641 (tm-30) REVERT: B 586 ASP cc_start: 0.7717 (m-30) cc_final: 0.7448 (m-30) REVERT: B 900 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8444 (mtm) REVERT: C 81 ASN cc_start: 0.8076 (p0) cc_final: 0.7791 (p0) REVERT: C 153 MET cc_start: 0.7048 (pmm) cc_final: 0.6571 (pp-130) REVERT: C 237 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6380 (mtp85) REVERT: C 529 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7907 (mmpt) REVERT: C 558 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7503 (mppt) REVERT: C 988 GLU cc_start: 0.6700 (tp30) cc_final: 0.6378 (tp30) outliers start: 69 outliers final: 32 residues processed: 220 average time/residue: 1.1009 time to fit residues: 293.7463 Evaluate side-chains 214 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.0070 chunk 75 optimal weight: 0.0980 chunk 307 optimal weight: 0.4980 chunk 255 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 26133 Z= 0.159 Angle : 0.508 13.515 35561 Z= 0.263 Chirality : 0.043 0.269 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.593 59.964 4305 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.69 % Allowed : 11.01 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3157 helix: 2.04 (0.21), residues: 658 sheet: 0.57 (0.19), residues: 730 loop : -1.37 (0.13), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 PHE 0.016 0.001 PHE A 565 TYR 0.017 0.001 TYR A1067 ARG 0.010 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 189 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 188 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7815 (p0) REVERT: A 378 LYS cc_start: 0.6850 (mttp) cc_final: 0.6302 (mtpp) REVERT: A 455 LEU cc_start: 0.8053 (tt) cc_final: 0.7731 (tm) REVERT: A 745 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6976 (p0) REVERT: A 916 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 129 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7573 (mmmt) REVERT: B 177 MET cc_start: 0.4147 (ttm) cc_final: 0.2180 (pmt) REVERT: C 81 ASN cc_start: 0.8006 (p0) cc_final: 0.7773 (p0) REVERT: C 153 MET cc_start: 0.7049 (pmm) cc_final: 0.6579 (pp-130) REVERT: C 237 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6461 (mtp-110) REVERT: C 529 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7911 (mmpt) REVERT: C 697 MET cc_start: 0.8228 (ptm) cc_final: 0.7961 (ptp) REVERT: C 988 GLU cc_start: 0.6593 (tp30) cc_final: 0.6292 (tp30) outliers start: 47 outliers final: 25 residues processed: 220 average time/residue: 1.0164 time to fit residues: 273.5064 Evaluate side-chains 204 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 174 optimal weight: 0.0370 chunk 259 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 564 GLN A 901 GLN A 969 ASN B 146 HIS B 334 ASN B 532 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26133 Z= 0.271 Angle : 0.569 13.109 35561 Z= 0.296 Chirality : 0.046 0.273 4143 Planarity : 0.004 0.050 4562 Dihedral : 5.683 59.353 4305 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.33 % Allowed : 11.22 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3157 helix: 1.84 (0.21), residues: 658 sheet: 0.55 (0.19), residues: 720 loop : -1.44 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.016 0.002 PHE A 565 TYR 0.024 0.001 TYR A1067 ARG 0.009 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 239 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: A 455 LEU cc_start: 0.8056 (tt) cc_final: 0.7746 (tm) REVERT: A 555 SER cc_start: 0.7386 (p) cc_final: 0.7172 (p) REVERT: A 745 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6974 (p0) REVERT: A 916 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8516 (tp) REVERT: B 129 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7233 (mmmt) REVERT: B 177 MET cc_start: 0.4279 (ttm) cc_final: 0.2333 (pmt) REVERT: B 314 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: B 619 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: C 81 ASN cc_start: 0.8023 (p0) cc_final: 0.7713 (p0) REVERT: C 153 MET cc_start: 0.7066 (pmm) cc_final: 0.6855 (pmm) REVERT: C 169 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: C 237 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6516 (mtp-110) REVERT: C 529 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7922 (mmpt) REVERT: C 558 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7515 (mppt) REVERT: C 988 GLU cc_start: 0.6720 (tp30) cc_final: 0.6384 (tp30) outliers start: 65 outliers final: 36 residues processed: 222 average time/residue: 1.0824 time to fit residues: 294.9647 Evaluate side-chains 219 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 240 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN B 334 ASN B 532 ASN C 234 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26133 Z= 0.202 Angle : 0.534 12.549 35561 Z= 0.277 Chirality : 0.044 0.269 4143 Planarity : 0.004 0.047 4562 Dihedral : 5.557 59.927 4303 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.97 % Allowed : 11.65 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3157 helix: 1.96 (0.21), residues: 659 sheet: 0.56 (0.19), residues: 723 loop : -1.42 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.016 0.001 PHE A 565 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.5357 (mtpp) cc_final: 0.5077 (ttmm) REVERT: A 177 MET cc_start: -0.0805 (pmm) cc_final: -0.1325 (ptp) REVERT: A 188 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7784 (p0) REVERT: A 378 LYS cc_start: 0.7057 (mttp) cc_final: 0.6818 (mttt) REVERT: A 455 LEU cc_start: 0.8064 (tt) cc_final: 0.7766 (tm) REVERT: A 745 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6973 (p0) REVERT: A 916 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8540 (tp) REVERT: B 129 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7745 (mmmt) REVERT: B 177 MET cc_start: 0.4282 (ttm) cc_final: 0.2348 (pmt) REVERT: B 979 ASP cc_start: 0.7247 (m-30) cc_final: 0.7035 (m-30) REVERT: C 81 ASN cc_start: 0.8013 (p0) cc_final: 0.7717 (p0) REVERT: C 169 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: C 237 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6423 (mtp85) REVERT: C 529 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7959 (mmpt) REVERT: C 988 GLU cc_start: 0.6639 (tp30) cc_final: 0.6335 (tp30) outliers start: 55 outliers final: 38 residues processed: 214 average time/residue: 0.9882 time to fit residues: 258.6337 Evaluate side-chains 212 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9990 chunk 293 optimal weight: 0.8980 chunk 267 optimal weight: 0.1980 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 258 optimal weight: 30.0000 chunk 270 optimal weight: 0.7980 chunk 284 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 969 ASN B 334 ASN B 532 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26133 Z= 0.183 Angle : 0.525 12.156 35561 Z= 0.271 Chirality : 0.044 0.263 4143 Planarity : 0.004 0.046 4562 Dihedral : 5.402 58.534 4303 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.83 % Allowed : 12.08 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3157 helix: 2.07 (0.21), residues: 659 sheet: 0.57 (0.19), residues: 716 loop : -1.39 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.001 PHE A 565 TYR 0.020 0.001 TYR A1067 ARG 0.010 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 178 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0490 (pmm) cc_final: -0.1016 (ptp) REVERT: A 188 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7769 (p0) REVERT: A 305 SER cc_start: 0.8687 (t) cc_final: 0.8412 (m) REVERT: A 378 LYS cc_start: 0.6963 (mttp) cc_final: 0.6713 (mttt) REVERT: A 455 LEU cc_start: 0.8116 (tt) cc_final: 0.7825 (tm) REVERT: A 745 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6963 (p0) REVERT: A 916 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8537 (tp) REVERT: B 129 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7630 (mmmt) REVERT: B 177 MET cc_start: 0.4167 (ttm) cc_final: 0.2348 (pmt) REVERT: B 576 VAL cc_start: 0.8704 (t) cc_final: 0.8495 (p) REVERT: C 80 ASP cc_start: 0.6729 (p0) cc_final: 0.5319 (m-30) REVERT: C 81 ASN cc_start: 0.7969 (p0) cc_final: 0.7639 (p0) REVERT: C 153 MET cc_start: 0.7081 (pmm) cc_final: 0.6534 (pp-130) REVERT: C 169 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: C 237 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6649 (mpp-170) REVERT: C 529 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7946 (mmpt) REVERT: C 988 GLU cc_start: 0.6625 (tp30) cc_final: 0.6313 (tp30) outliers start: 51 outliers final: 39 residues processed: 215 average time/residue: 1.0284 time to fit residues: 270.8417 Evaluate side-chains 212 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 chunk 143 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 0.0970 chunk 291 optimal weight: 0.6980 chunk 252 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 969 ASN B 66 HIS B 334 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26133 Z= 0.205 Angle : 0.543 12.045 35561 Z= 0.281 Chirality : 0.044 0.263 4143 Planarity : 0.004 0.048 4562 Dihedral : 5.406 59.224 4303 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.65 % Allowed : 12.41 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3157 helix: 2.02 (0.21), residues: 659 sheet: 0.55 (0.19), residues: 713 loop : -1.39 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 64 HIS 0.006 0.001 HIS B 207 PHE 0.016 0.001 PHE A 565 TYR 0.021 0.001 TYR A1067 ARG 0.010 0.000 ARG C 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6314 Ramachandran restraints generated. 3157 Oldfield, 0 Emsley, 3157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 171 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.0525 (pmm) cc_final: -0.1043 (ptp) REVERT: A 188 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 305 SER cc_start: 0.8689 (t) cc_final: 0.8411 (m) REVERT: A 378 LYS cc_start: 0.7064 (mttp) cc_final: 0.6814 (mttt) REVERT: A 455 LEU cc_start: 0.8102 (tt) cc_final: 0.7811 (tm) REVERT: A 556 ASN cc_start: 0.7310 (p0) cc_final: 0.6796 (p0) REVERT: A 745 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6958 (p0) REVERT: A 916 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8530 (tp) REVERT: B 129 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7625 (mmmt) REVERT: B 177 MET cc_start: 0.4165 (ttm) cc_final: 0.2333 (pmt) REVERT: B 190 ARG cc_start: 0.6807 (mmm160) cc_final: 0.6499 (mmp80) REVERT: C 81 ASN cc_start: 0.7972 (p0) cc_final: 0.7637 (p0) REVERT: C 169 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: C 237 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6422 (mtp85) REVERT: C 529 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7947 (mmpt) REVERT: C 988 GLU cc_start: 0.6653 (tp30) cc_final: 0.6327 (tp30) outliers start: 46 outliers final: 38 residues processed: 204 average time/residue: 0.9990 time to fit residues: 249.1740 Evaluate side-chains 210 residues out of total 2789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 901 GLN A 969 ASN B 122 ASN B 532 ASN C 394 ASN C 556 ASN C 675 GLN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.200495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133225 restraints weight = 29165.017| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.20 r_work: 0.3247 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26133 Z= 0.280 Angle : 0.586 11.996 35561 Z= 0.304 Chirality : 0.046 0.269 4143 Planarity : 0.004 0.050 4562 Dihedral : 5.564 59.636 4303 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 12.48 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3157 helix: 1.79 (0.21), residues: 658 sheet: 0.49 (0.19), residues: 714 loop : -1.46 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.018 0.002 PHE A 565 TYR 0.023 0.001 TYR A1067 ARG 0.010 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7111.23 seconds wall clock time: 128 minutes 40.58 seconds (7720.58 seconds total)