Starting phenix.real_space_refine on Wed Mar 20 06:27:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tgw_25887/03_2024/7tgw_25887.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 119 5.16 5 C 16993 2.51 5 N 4383 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 933": "OD1" <-> "OD2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A GLU 1141": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 827": "OD1" <-> "OD2" Residue "C PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 836": "OD1" <-> "OD2" Residue "C GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26617 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8741 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1113, 8725 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 61, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1113, 8725 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 61, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8918 Chain: "B" Number of atoms: 8579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1091, 8563 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 60, 'TRANS': 1030} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1091, 8563 Classifications: {'peptide': 1091} Link IDs: {'PTRANS': 60, 'TRANS': 1030} Chain breaks: 4 bond proxies already assigned to first conformer: 8751 Chain: "C" Number of atoms: 8667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1103, 8651 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 60, 'TRANS': 1042} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1103, 8651 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 60, 'TRANS': 1042} Chain breaks: 3 bond proxies already assigned to first conformer: 8841 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 23.80, per 1000 atoms: 0.89 Number of scatterers: 26617 At special positions: 0 Unit cell: (152.19, 150.41, 201.14, 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 119 16.00 O 5122 8.00 N 4383 7.00 C 16993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.04 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.04 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.00 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.02 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.04 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.04 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.05 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.05 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.05 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.05 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 Atom "HETATM26027 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. 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 L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 160 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 279 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1305 " - " ASN B 654 " " NAG B1307 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 714 " " NAG C1304 " - " ASN C 279 " " NAG C1305 " - " ASN C 706 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 714 " " NAG F 1 " - " ASN A 798 " " NAG G 1 " - " ASN A1095 " " NAG H 1 " - " ASN A1131 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG L 1 " - " ASN B1131 " " NAG M 1 " - " ASN C 798 " " NAG N 1 " - " ASN C1095 " " NAG O 1 " - " ASN C1131 " Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 8.4 seconds 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 50 sheets defined 23.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.646A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.944A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.726A pdb=" N LEU A 626 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 751 removed outlier: 3.803A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.783A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 removed outlier: 3.853A pdb=" N LEU A 818 " --> pdb=" O PRO A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 882 removed outlier: 3.591A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.501A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.943A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.687A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.584A pdb=" N ALA A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.691A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 947 " --> pdb=" O GLY A 943 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 5.248A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.304A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 499 through 502 removed outlier: 3.588A pdb=" N HIS B 502 " --> pdb=" O GLY B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 744 through 751 removed outlier: 3.662A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.793A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.840A pdb=" N LEU B 818 " --> pdb=" O PRO B 814 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 853 removed outlier: 3.670A pdb=" N LYS B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 removed outlier: 3.571A pdb=" N ILE B 867 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.542A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 907 removed outlier: 3.716A pdb=" N ALA B 900 " --> pdb=" O PRO B 896 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.822A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 937 removed outlier: 3.590A pdb=" N LEU B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.942A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.730A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.026A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.762A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.975A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.614A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.180A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 removed outlier: 4.000A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.854A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 838 through 842 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.591A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.600A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 896 No H-bonds generated for 'chain 'C' and resid 894 through 896' Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.949A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.708A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.849A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 4.213A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 5.390A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.226A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 183 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 224 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N HIS A 202 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU A 220 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.076A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.940A pdb=" N ARG A 234 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 104 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLN A 236 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP A 102 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 238 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN A 119 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 128 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER A 157 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ASP A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR A 155 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 12.452A pdb=" N PHE A 235 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 12.858A pdb=" N ASN A 135 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N THR A 237 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU A 239 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 124 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 128 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER A 157 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N ASP A 136 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR A 155 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 7.261A pdb=" N ALA A 345 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ARG A 400 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 346 removed outlier: 7.261A pdb=" N ALA A 345 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ARG A 400 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 393 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 506 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 removed outlier: 3.626A pdb=" N ARG A 490 " --> pdb=" O TYR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 536 through 540 removed outlier: 6.001A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.211A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 688 " --> pdb=" O GLN A 672 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 698 through 699 removed outlier: 7.124A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 709 removed outlier: 3.662A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.068A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.280A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N HIS B 202 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N LEU B 220 " --> pdb=" O HIS B 202 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 36 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.984A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.820A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 131 through 133 removed outlier: 4.919A pdb=" N SER B 157 " --> pdb=" O GLN B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 312 removed outlier: 4.391A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.658A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.930A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 Processing sheet with id=AC9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.715A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 562 through 563 removed outlier: 7.463A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.278A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 698 through 699 removed outlier: 7.000A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.022A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD7, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.649A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.081A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.053A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.743A pdb=" N GLN C 236 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 128 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 147 through 152 removed outlier: 5.422A pdb=" N GLU C 149 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 142 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 241 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS C 141 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG C 243 " --> pdb=" O HIS C 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 313 removed outlier: 7.099A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.860A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.860A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 521 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 536 through 540 removed outlier: 3.537A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 584 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.142A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.945A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF5, first strand: chain 'C' and resid 1091 through 1094 915 hydrogen bonds defined for protein. 2481 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: 10.26 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8444 1.34 - 1.47: 6923 1.47 - 1.59: 11738 1.59 - 1.72: 1 1.72 - 1.84: 148 Bond restraints: 27254 Sorted by residual: bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.564 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta sigma weight residual 1.457 1.511 -0.054 1.29e-02 6.01e+03 1.76e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N VAL B 632 " pdb=" CA VAL B 632 " ideal model delta sigma weight residual 1.462 1.496 -0.033 1.06e-02 8.90e+03 9.99e+00 bond pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.41e-02 5.03e+03 9.90e+00 ... (remaining 27249 not shown) Histogram of bond angle deviations from ideal: 99.28 - 107.49: 1087 107.49 - 115.70: 16688 115.70 - 123.91: 18678 123.91 - 132.12: 615 132.12 - 140.33: 31 Bond angle restraints: 37099 Sorted by residual: angle pdb=" CA CYS C 522 " pdb=" CB CYS C 522 " pdb=" SG CYS C 522 " ideal model delta sigma weight residual 114.40 140.33 -25.93 2.30e+00 1.89e-01 1.27e+02 angle pdb=" N PRO A 319 " pdb=" CA PRO A 319 " pdb=" C PRO A 319 " ideal model delta sigma weight residual 113.47 122.80 -9.33 1.43e+00 4.89e-01 4.26e+01 angle pdb=" C TYR B 633 " pdb=" N SER B 634 " pdb=" CA SER B 634 " ideal model delta sigma weight residual 122.67 132.73 -10.06 1.73e+00 3.34e-01 3.38e+01 angle pdb=" C THR A 713 " pdb=" N ASN A 714 " pdb=" CA ASN A 714 " ideal model delta sigma weight residual 122.11 130.98 -8.87 1.59e+00 3.96e-01 3.11e+01 angle pdb=" N ASP B 140 " pdb=" CA ASP B 140 " pdb=" CB ASP B 140 " ideal model delta sigma weight residual 110.49 101.51 8.98 1.69e+00 3.50e-01 2.82e+01 ... (remaining 37094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 15910 23.67 - 47.33: 709 47.33 - 71.00: 176 71.00 - 94.66: 56 94.66 - 118.33: 33 Dihedral angle restraints: 16884 sinusoidal: 7221 harmonic: 9663 Sorted by residual: dihedral pdb=" CA CYS A 614 " pdb=" C CYS A 614 " pdb=" N THR A 615 " pdb=" CA THR A 615 " ideal model delta harmonic sigma weight residual 180.00 127.75 52.25 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CB CYS C 614 " pdb=" SG CYS C 614 " pdb=" SG CYS C 646 " pdb=" CB CYS C 646 " ideal model delta sinusoidal sigma weight residual 93.00 7.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 614 " pdb=" SG CYS A 614 " pdb=" SG CYS A 646 " pdb=" CB CYS A 646 " ideal model delta sinusoidal sigma weight residual 93.00 169.93 -76.93 1 1.00e+01 1.00e-02 7.43e+01 ... (remaining 16881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.085: 4297 1.085 - 2.170: 0 2.170 - 3.254: 0 3.254 - 4.339: 0 4.339 - 5.424: 1 Chirality restraints: 4298 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 3.02 -5.42 2.00e-01 2.50e+01 7.35e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 8.61e+00 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 706 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 4295 not shown) Planarity restraints: 4776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 714 " 0.066 2.00e-02 2.50e+03 6.61e-02 5.47e+01 pdb=" CG ASN A 714 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 714 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 714 " -0.074 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.001 2.00e-02 2.50e+03 6.38e-02 5.08e+01 pdb=" CG ASN A 61 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 140 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ASP A 140 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP A 140 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 141 " 0.024 2.00e-02 2.50e+03 ... (remaining 4773 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 251 2.57 - 3.15: 21691 3.15 - 3.73: 35894 3.73 - 4.32: 52169 4.32 - 4.90: 89627 Nonbonded interactions: 199632 Sorted by model distance: nonbonded pdb=" O3 NAG I 2 " pdb=" O7 NAG I 2 " model vdw 1.983 2.440 nonbonded pdb=" NZ LYS B 808 " pdb=" OD2 ASP B 817 " model vdw 2.007 2.520 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.021 2.440 nonbonded pdb=" OD2 ASP C 840 " pdb=" NH1 ARG C 844 " model vdw 2.029 2.520 nonbonded pdb=" NH1 ARG B 208 " pdb=" O GLU B 209 " model vdw 2.092 2.520 ... (remaining 199627 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 618 or resid 630 through 819 or resid 821 throu \ gh 832 or resid 845 through 1015 or resid 1017 through 1143 or resid 1301 throug \ h 1306)) selection = (chain 'B' and (resid 14 through 618 or resid 630 through 819 or resid 821 throu \ gh 1015 or resid 1017 through 1143 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 618 or resid 630 through 819 or resid 821 throu \ gh 832 or resid 845 through 1015 or resid 1017 through 1143 or resid 1301 throug \ h 1306)) } 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' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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=0.50 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: 12.800 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 80.890 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.300 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:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.007 0.158 27254 Z= 0.478 Angle : 0.855 25.934 37099 Z= 0.470 Chirality : 0.098 5.424 4298 Planarity : 0.006 0.069 4749 Dihedral : 15.753 118.331 10542 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 0.24 % Allowed : 0.41 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.46 (0.13), residues: 3289 helix: -0.09 (0.20), residues: 653 sheet: -0.51 (0.20), residues: 617 loop : -2.71 (0.11), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 883 HIS 0.014 0.002 HIS C 951 PHE 0.026 0.002 PHE B 640 TYR 0.033 0.002 TYR B 753 ARG 0.012 0.001 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.7724 (t80) cc_final: 0.7377 (t80) REVERT: A 529 ASN cc_start: 0.7947 (m-40) cc_final: 0.7651 (m-40) REVERT: A 755 SER cc_start: 0.8529 (m) cc_final: 0.8219 (p) REVERT: B 172 MET cc_start: 0.3347 (mtt) cc_final: 0.2910 (mtt) REVERT: B 516 HIS cc_start: 0.8252 (m90) cc_final: 0.7890 (m90) REVERT: B 633 TYR cc_start: 0.5127 (m-10) cc_final: 0.4231 (m-10) REVERT: C 172 MET cc_start: 0.4331 (mtt) cc_final: 0.3922 (mtp) outliers start: 6 outliers final: 0 residues processed: 199 average time/residue: 1.5311 time to fit residues: 351.3985 Evaluate side-chains 101 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS A 503 GLN A 672 GLN A 923 GLN A1116 ASN B 14 GLN B 144 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 916 ASN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 236 GLN C 391 ASN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 HIS C 999 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27254 Z= 0.296 Angle : 0.771 13.372 37099 Z= 0.384 Chirality : 0.055 1.471 4298 Planarity : 0.005 0.057 4749 Dihedral : 11.774 106.648 4520 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 0.76 % Allowed : 5.41 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3289 helix: 0.82 (0.21), residues: 644 sheet: 0.04 (0.21), residues: 620 loop : -2.45 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 147 HIS 0.012 0.001 HIS B 242 PHE 0.015 0.002 PHE A 77 TYR 0.022 0.001 TYR B 492 ARG 0.012 0.001 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TYR cc_start: 0.7536 (t80) cc_final: 0.7085 (t80) REVERT: A 172 MET cc_start: -0.0977 (mmt) cc_final: -0.1454 (mtp) REVERT: A 991 ASP cc_start: 0.8143 (t70) cc_final: 0.7926 (t0) REVERT: B 172 MET cc_start: 0.3061 (mtt) cc_final: 0.1772 (mpt) REVERT: B 516 HIS cc_start: 0.8133 (m90) cc_final: 0.7802 (m90) REVERT: C 195 TYR cc_start: 0.7971 (m-80) cc_final: 0.7624 (m-80) REVERT: C 999 GLN cc_start: 0.8097 (tp40) cc_final: 0.7827 (tp-100) outliers start: 21 outliers final: 8 residues processed: 132 average time/residue: 1.1953 time to fit residues: 189.7678 Evaluate side-chains 109 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 938 THR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 300 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 297 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 144 ASN A 672 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27254 Z= 0.285 Angle : 0.707 15.981 37099 Z= 0.353 Chirality : 0.050 0.728 4298 Planarity : 0.005 0.050 4749 Dihedral : 9.083 97.976 4520 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 1.00 % Allowed : 6.79 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3289 helix: 1.11 (0.21), residues: 660 sheet: 0.18 (0.21), residues: 616 loop : -2.36 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 883 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE A 77 TYR 0.026 0.001 TYR B 492 ARG 0.008 0.001 ARG B 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0792 (mmt) cc_final: -0.1826 (mtt) REVERT: B 172 MET cc_start: 0.3031 (mtt) cc_final: 0.2759 (mtt) REVERT: B 513 GLU cc_start: 0.7952 (tp30) cc_final: 0.7186 (tm-30) REVERT: B 514 LEU cc_start: 0.7945 (mt) cc_final: 0.7582 (mm) REVERT: B 866 MET cc_start: 0.8801 (mtt) cc_final: 0.8502 (mtt) REVERT: C 100 ARG cc_start: 0.6447 (mtt180) cc_final: 0.5280 (mtt180) REVERT: C 116 LEU cc_start: 0.7178 (mp) cc_final: 0.6866 (mm) REVERT: C 195 TYR cc_start: 0.8161 (m-80) cc_final: 0.7746 (m-80) outliers start: 28 outliers final: 19 residues processed: 140 average time/residue: 1.1556 time to fit residues: 196.7231 Evaluate side-chains 122 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 33 optimal weight: 40.0000 chunk 143 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 30.0000 chunk 285 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 GLN A 999 GLN B 14 GLN B 30 ASN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN C 242 HIS C 610 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 27254 Z= 0.352 Angle : 0.715 16.530 37099 Z= 0.360 Chirality : 0.050 0.624 4298 Planarity : 0.005 0.051 4749 Dihedral : 8.581 92.850 4520 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 1.00 % Allowed : 7.82 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3289 helix: 1.18 (0.22), residues: 658 sheet: 0.29 (0.21), residues: 614 loop : -2.34 (0.12), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 883 HIS 0.009 0.001 HIS B 516 PHE 0.036 0.002 PHE A 152 TYR 0.024 0.001 TYR A 165 ARG 0.007 0.001 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0675 (mmt) cc_final: -0.1204 (mtt) REVERT: A 985 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7553 (mp0) REVERT: B 172 MET cc_start: 0.3178 (mtt) cc_final: 0.2858 (mtt) REVERT: B 513 GLU cc_start: 0.8452 (tp30) cc_final: 0.8187 (tp30) REVERT: B 516 HIS cc_start: 0.8362 (m-70) cc_final: 0.8110 (m90) REVERT: B 866 MET cc_start: 0.8832 (mtt) cc_final: 0.8553 (mtt) REVERT: C 195 TYR cc_start: 0.8174 (m-80) cc_final: 0.7729 (m-80) REVERT: C 498 TYR cc_start: 0.8301 (m-80) cc_final: 0.8079 (m-80) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 1.2778 time to fit residues: 189.5232 Evaluate side-chains 115 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 672 GLN Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 220 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 162 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27254 Z= 0.303 Angle : 0.675 12.948 37099 Z= 0.340 Chirality : 0.049 0.565 4298 Planarity : 0.005 0.048 4749 Dihedral : 8.169 89.756 4520 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.55 % Favored : 93.42 % Rotamer: Outliers : 1.10 % Allowed : 8.34 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3289 helix: 1.37 (0.22), residues: 649 sheet: 0.33 (0.21), residues: 604 loop : -2.24 (0.12), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 255 HIS 0.004 0.001 HIS A 66 PHE 0.031 0.002 PHE A 152 TYR 0.020 0.001 TYR B 492 ARG 0.007 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0623 (mmt) cc_final: -0.0962 (mtt) REVERT: B 172 MET cc_start: 0.3089 (mtt) cc_final: 0.2813 (mtt) REVERT: B 513 GLU cc_start: 0.8459 (tp30) cc_final: 0.8158 (tp30) REVERT: B 516 HIS cc_start: 0.8312 (m-70) cc_final: 0.8073 (m90) REVERT: B 866 MET cc_start: 0.8794 (mtt) cc_final: 0.8494 (mtt) REVERT: C 195 TYR cc_start: 0.8178 (m-80) cc_final: 0.7797 (m-80) REVERT: C 632 VAL cc_start: 0.8018 (m) cc_final: 0.7802 (p) outliers start: 31 outliers final: 25 residues processed: 130 average time/residue: 1.1336 time to fit residues: 179.4755 Evaluate side-chains 125 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 77 PHE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 753 TYR Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.9980 chunk 287 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 167 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27254 Z= 0.165 Angle : 0.614 12.101 37099 Z= 0.305 Chirality : 0.046 0.507 4298 Planarity : 0.004 0.044 4749 Dihedral : 7.129 84.944 4520 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 0.90 % Allowed : 8.86 % Favored : 90.24 % 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: -1.12 (0.14), residues: 3289 helix: 1.71 (0.22), residues: 656 sheet: 0.35 (0.21), residues: 630 loop : -2.11 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 255 HIS 0.004 0.001 HIS A 66 PHE 0.029 0.001 PHE A 152 TYR 0.021 0.001 TYR A 165 ARG 0.009 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0747 (mmt) cc_final: -0.1117 (mtt) REVERT: B 492 TYR cc_start: 0.7485 (m-10) cc_final: 0.6558 (m-10) REVERT: B 513 GLU cc_start: 0.8423 (tp30) cc_final: 0.8186 (tp30) REVERT: B 516 HIS cc_start: 0.8213 (m90) cc_final: 0.7952 (m90) REVERT: B 866 MET cc_start: 0.8612 (mtt) cc_final: 0.8292 (mtt) REVERT: C 100 ARG cc_start: 0.6607 (mtt180) cc_final: 0.6373 (mtm180) REVERT: C 195 TYR cc_start: 0.8089 (m-80) cc_final: 0.7783 (m-80) REVERT: C 516 HIS cc_start: 0.7466 (m-70) cc_final: 0.7258 (m-70) REVERT: C 632 VAL cc_start: 0.8056 (m) cc_final: 0.7788 (p) outliers start: 25 outliers final: 12 residues processed: 138 average time/residue: 1.2343 time to fit residues: 206.9667 Evaluate side-chains 117 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 181 optimal weight: 0.0570 chunk 233 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27254 Z= 0.265 Angle : 0.639 10.378 37099 Z= 0.321 Chirality : 0.048 0.509 4298 Planarity : 0.004 0.046 4749 Dihedral : 6.987 81.683 4520 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 0.72 % Allowed : 9.55 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3289 helix: 1.67 (0.22), residues: 659 sheet: 0.40 (0.21), residues: 605 loop : -2.14 (0.12), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 102 HIS 0.004 0.001 HIS B 242 PHE 0.056 0.001 PHE B 77 TYR 0.021 0.001 TYR C1135 ARG 0.009 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0682 (mmt) cc_final: -0.1161 (mtt) REVERT: A 985 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7411 (mp0) REVERT: B 172 MET cc_start: 0.1591 (mtt) cc_final: 0.0623 (mpt) REVERT: B 449 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6732 (pp) REVERT: B 516 HIS cc_start: 0.8194 (m90) cc_final: 0.7913 (m90) REVERT: B 866 MET cc_start: 0.8747 (mtt) cc_final: 0.8415 (mtt) REVERT: C 195 TYR cc_start: 0.8128 (m-80) cc_final: 0.7762 (m-80) REVERT: C 516 HIS cc_start: 0.7497 (m-70) cc_final: 0.7297 (m-70) REVERT: C 632 VAL cc_start: 0.8011 (m) cc_final: 0.7772 (p) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 1.1513 time to fit residues: 168.9468 Evaluate side-chains 118 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 157 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27254 Z= 0.218 Angle : 0.621 10.397 37099 Z= 0.311 Chirality : 0.047 0.493 4298 Planarity : 0.004 0.046 4749 Dihedral : 6.826 78.589 4520 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 0.69 % Allowed : 9.79 % Favored : 89.52 % 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: -1.08 (0.14), residues: 3289 helix: 1.75 (0.22), residues: 656 sheet: 0.37 (0.21), residues: 620 loop : -2.08 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 102 HIS 0.004 0.001 HIS B 242 PHE 0.029 0.001 PHE B 372 TYR 0.020 0.001 TYR B 492 ARG 0.008 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7715 (m-10) cc_final: 0.7377 (m-10) REVERT: A 172 MET cc_start: -0.0809 (mmt) cc_final: -0.1090 (mtt) REVERT: A 985 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7532 (mp0) REVERT: B 172 MET cc_start: 0.1557 (mtt) cc_final: 0.0253 (mpt) REVERT: B 513 GLU cc_start: 0.8305 (tp30) cc_final: 0.8035 (tp30) REVERT: B 866 MET cc_start: 0.8696 (mtt) cc_final: 0.8372 (mtt) REVERT: C 195 TYR cc_start: 0.8135 (m-80) cc_final: 0.7796 (m-80) REVERT: C 632 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7778 (p) outliers start: 20 outliers final: 18 residues processed: 124 average time/residue: 1.1917 time to fit residues: 179.3580 Evaluate side-chains 123 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 278 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27254 Z= 0.176 Angle : 0.609 12.043 37099 Z= 0.303 Chirality : 0.046 0.478 4298 Planarity : 0.004 0.045 4749 Dihedral : 6.653 74.834 4520 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.79 % Allowed : 9.93 % Favored : 89.28 % 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: -0.98 (0.15), residues: 3289 helix: 1.89 (0.22), residues: 656 sheet: 0.40 (0.21), residues: 620 loop : -2.02 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 102 HIS 0.004 0.001 HIS B 242 PHE 0.028 0.001 PHE B 372 TYR 0.018 0.001 TYR C1135 ARG 0.009 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0504 (mmt) cc_final: -0.0801 (mtt) REVERT: A 985 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7554 (mp0) REVERT: B 172 MET cc_start: 0.1204 (mtt) cc_final: 0.0239 (mpt) REVERT: B 866 MET cc_start: 0.8653 (mtt) cc_final: 0.8359 (mtt) REVERT: C 100 ARG cc_start: 0.6717 (mtt180) cc_final: 0.5512 (mtt180) REVERT: C 195 TYR cc_start: 0.8113 (m-80) cc_final: 0.7813 (m-80) REVERT: C 632 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7584 (p) outliers start: 23 outliers final: 18 residues processed: 126 average time/residue: 1.2000 time to fit residues: 186.2570 Evaluate side-chains 119 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 397 PHE Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 217 optimal weight: 0.7980 chunk 328 optimal weight: 0.2980 chunk 302 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 202 optimal weight: 0.2980 chunk 160 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 66 HIS B 113 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27254 Z= 0.158 Angle : 0.596 12.898 37099 Z= 0.297 Chirality : 0.046 0.466 4298 Planarity : 0.004 0.043 4749 Dihedral : 6.495 71.178 4520 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 0.69 % Allowed : 10.24 % Favored : 89.07 % 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: -0.85 (0.15), residues: 3289 helix: 2.13 (0.22), residues: 644 sheet: 0.46 (0.21), residues: 631 loop : -1.97 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 PHE 0.056 0.001 PHE B 77 TYR 0.019 0.001 TYR A 165 ARG 0.009 0.000 ARG B 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6578 Ramachandran restraints generated. 3289 Oldfield, 0 Emsley, 3289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: -0.0352 (mmt) cc_final: -0.0727 (mtt) REVERT: A 985 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7589 (mp0) REVERT: B 172 MET cc_start: 0.1381 (mtt) cc_final: 0.0265 (mpt) REVERT: B 343 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8205 (tpm170) REVERT: B 866 MET cc_start: 0.8585 (mtt) cc_final: 0.8278 (mtt) REVERT: C 195 TYR cc_start: 0.8087 (m-80) cc_final: 0.7872 (m-80) REVERT: C 632 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (p) outliers start: 20 outliers final: 16 residues processed: 125 average time/residue: 1.1800 time to fit residues: 177.3148 Evaluate side-chains 122 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 714 ASN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 448 TYR Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 0.6980 chunk 278 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 241 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 109 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.124494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069694 restraints weight = 106237.165| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 5.41 r_work: 0.2734 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27254 Z= 0.271 Angle : 0.642 12.616 37099 Z= 0.324 Chirality : 0.047 0.474 4298 Planarity : 0.004 0.069 4749 Dihedral : 6.598 67.760 4520 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 0.72 % Allowed : 10.27 % Favored : 89.00 % 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: -0.98 (0.15), residues: 3289 helix: 1.81 (0.22), residues: 657 sheet: 0.44 (0.21), residues: 625 loop : -2.01 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 102 HIS 0.006 0.001 HIS B 242 PHE 0.033 0.002 PHE C 453 TYR 0.019 0.001 TYR B1064 ARG 0.014 0.001 ARG B 631 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6270.85 seconds wall clock time: 113 minutes 12.52 seconds (6792.52 seconds total)