Starting phenix.real_space_refine on Sat Mar 7 14:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094.map" model { file = "/net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l02_23094/03_2026/7l02_23094_neut_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.003 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 19220 2.51 5 N 4947 2.21 5 O 5979 1.98 5 H 13841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44110 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 15044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 15044 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "B" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "H" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3251 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "K" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3230 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "L" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3200 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3247 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 3, 'MAN': 3, 'NAG': 2} 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: "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: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 9.06, per 1000 atoms: 0.21 Number of scatterers: 44110 At special positions: 0 Unit cell: (134.366, 155.526, 212.658, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 5979 8.00 N 4947 7.00 C 19220 6.00 H 13841 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.12 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.88 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.16 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.00 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.06 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.08 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.26 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.10 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.13 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.06 Simple disulfide: pdb=" SG CYS M 142 " - pdb=" SG CYS M 208 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 5 " - " MAN F 6 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " BETA1-3 " BMA F 3 " - " BMA F 8 " " MAN F 4 " - " BMA F 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " BETA1-6 " BMA T 3 " - " BMA T 5 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 165 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 709 " " NAG B1201 " - " ASN B 282 " " NAG B1202 " - " ASN B 331 " " NAG B1203 " - " ASN B 343 " " NAG B1204 " - " ASN B 603 " " NAG B1205 " - " ASN B 616 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 709 " " NAG B1208 " - " ASN B1074 " " NAG B1209 " - " ASN B 165 " " NAG B1210 " - " ASN B 61 " " NAG B1211 " - " ASN B 122 " " NAG C1201 " - " ASN C 657 " " NAG C1202 " - " ASN C1074 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 122 " " NAG C1206 " - " ASN C 282 " " NAG C1207 " - " ASN C 331 " " NAG C1208 " - " ASN C 343 " " NAG C1209 " - " ASN C 603 " " NAG C1210 " - " ASN C 616 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 709 " Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 67 sheets defined 21.7% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.891A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.228A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.198A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.900A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.577A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.581A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.538A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.889A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.229A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.916A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.889A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.569A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.227A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.975A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.806A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.914A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.799A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 52A through 55 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 199 removed outlier: 3.988A pdb=" N GLY H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 199' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE K 83 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 4.049A pdb=" N SER K 127 " --> pdb=" O GLU K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.503A pdb=" N PHE L 83 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.058A pdb=" N ALA M 31 " --> pdb=" O ARG M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 52A through 55 removed outlier: 3.629A pdb=" N THR M 55 " --> pdb=" O THR M 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 52A through 55' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 163 through 165 No H-bonds generated for 'chain 'M' and resid 163 through 165' Processing helix chain 'M' and resid 196 through 199 removed outlier: 4.179A pdb=" N GLY M 199 " --> pdb=" O SER M 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 196 through 199' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.221A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.220A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.210A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.269A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.539A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.123A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.845A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.345A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 715 removed outlier: 4.469A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.821A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.500A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.009A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.366A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.727A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.531A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.240A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.801A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.847A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.631A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.497A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.692A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.008A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.367A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.728A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.529A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.239A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.122A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.755A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.847A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.023A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.405A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.496A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.690A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.604A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE H 89 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.604A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N SER H 112 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.209A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 152 through 157 removed outlier: 3.865A pdb=" N TYR H 206 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.337A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS K 50 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.564A pdb=" N SER K 95 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 115 through 118 removed outlier: 4.302A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER K 174 " --> pdb=" O THR K 164 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.690A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.511A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.622A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AG8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET M 34 " --> pdb=" O SER M 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.674A pdb=" N VAL M 12 " --> pdb=" O SER M 112 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 120 through 124 removed outlier: 6.148A pdb=" N TYR M 185 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 153 through 157 removed outlier: 4.279A pdb=" N TYR M 206 " --> pdb=" O VAL M 225 " (cutoff:3.500A) 1342 hydrogen bonds defined for protein. 3651 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: 14.79 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13814 1.04 - 1.25: 4840 1.25 - 1.46: 10716 1.46 - 1.66: 15237 1.66 - 1.87: 155 Bond restraints: 44762 Sorted by residual: bond pdb=" C ILE A1081 " pdb=" O ILE A1081 " ideal model delta sigma weight residual 1.236 1.164 0.072 9.90e-03 1.02e+04 5.24e+01 bond pdb=" NE ARG A 454 " pdb=" CZ ARG A 454 " ideal model delta sigma weight residual 1.326 1.389 -0.063 1.10e-02 8.26e+03 3.27e+01 bond pdb=" C VAL H 144 " pdb=" O VAL H 144 " ideal model delta sigma weight residual 1.238 1.172 0.066 1.17e-02 7.31e+03 3.20e+01 bond pdb=" NE ARG B 454 " pdb=" CZ ARG B 454 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.10e-02 8.26e+03 3.13e+01 bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.387 -0.061 1.10e-02 8.26e+03 3.03e+01 ... (remaining 44757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.33: 73358 10.33 - 20.66: 18 20.66 - 30.99: 0 30.99 - 41.32: 0 41.32 - 51.65: 2 Bond angle restraints: 73378 Sorted by residual: angle pdb=" CA ASN A 709 " pdb=" N ASN A 709 " pdb=" H ASN A 709 " ideal model delta sigma weight residual 114.71 63.06 51.65 3.00e+00 1.11e-01 2.96e+02 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" H ASN A 709 " ideal model delta sigma weight residual 125.01 76.77 48.24 3.00e+00 1.11e-01 2.59e+02 angle pdb=" C SER A 708 " pdb=" N ASN A 709 " pdb=" CA ASN A 709 " ideal model delta sigma weight residual 120.28 139.74 -19.46 1.44e+00 4.82e-01 1.83e+02 angle pdb=" CA SER A 708 " pdb=" C SER A 708 " pdb=" N ASN A 709 " ideal model delta sigma weight residual 115.61 127.76 -12.15 1.45e+00 4.76e-01 7.02e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.87 127.52 -7.65 1.04e+00 9.25e-01 5.41e+01 ... (remaining 73373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 23085 22.27 - 44.53: 823 44.53 - 66.80: 243 66.80 - 89.07: 98 89.07 - 111.34: 25 Dihedral angle restraints: 24274 sinusoidal: 12316 harmonic: 11958 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.94 86.94 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual -86.00 -0.30 -85.70 1 1.00e+01 1.00e-02 8.88e+01 ... (remaining 24271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.465: 5010 0.465 - 0.929: 2 0.929 - 1.393: 1 1.393 - 1.858: 0 1.858 - 2.322: 1 Chirality restraints: 5014 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.08 -2.32 2.00e-01 2.50e+01 1.35e+02 chirality pdb=" C1 BMA F 8 " pdb=" O3 BMA F 3 " pdb=" C2 BMA F 8 " pdb=" O5 BMA F 8 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.12e+01 ... (remaining 5011 not shown) Planarity restraints: 7080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A1106 " 0.226 2.00e-02 2.50e+03 2.72e-01 1.11e+03 pdb=" CD GLN A1106 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN A1106 " -0.228 2.00e-02 2.50e+03 pdb=" NE2 GLN A1106 " 0.007 2.00e-02 2.50e+03 pdb="HE21 GLN A1106 " -0.414 2.00e-02 2.50e+03 pdb="HE22 GLN A1106 " 0.411 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.332 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG G 1 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.093 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " 0.334 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG T 2 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.203 2.00e-02 2.50e+03 ... (remaining 7077 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 790 2.14 - 2.76: 52762 2.76 - 3.37: 96432 3.37 - 3.99: 137403 3.99 - 4.60: 205745 Nonbonded interactions: 493132 Sorted by model distance: nonbonded pdb=" H ASN A 709 " pdb=" HA ASN A 709 " model vdw 1.526 1.816 nonbonded pdb=" O GLN L 124 " pdb=" HG SER L 127 " model vdw 1.678 2.450 nonbonded pdb=" H ASN M 162 " pdb=" O ILE M 207 " model vdw 1.710 2.450 nonbonded pdb=" OD1 ASP K 170 " pdb=" HG1 THR K 172 " model vdw 1.717 2.450 nonbonded pdb=" H LYS A 97 " pdb=" H SER A 98 " model vdw 1.725 2.100 ... (remaining 493127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 27 and (name N or name CA or name C or name O or name CB \ )) or (resid 28 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (re \ sid 29 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 30 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name ND2)) or (resid 31 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 32 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ )) or (resid 33 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2)) or (resid 34 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2) \ ) or (resid 35 and (name N or name CA or name C or name O )) or (resid 36 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 37 through 38 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or ( \ resid 39 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD )) or (resid 40 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2)) or (resid 41 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 42 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r (resid 43 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 44 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name NE o \ r name CZ or name NH1 or name NH2)) or (resid 45 through 46 and (name N or name \ CA or name C or name O or name CB or name OG )) or (resid 47 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 48 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD1 or name C \ D2)) or (resid 49 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 50 and (name N or \ name CA or name C or name O or name CB or name OG )) or (resid 51 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 52 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name NE2)) or (resid 53 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 54 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid \ 55 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 56 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or (resid 58 through 59 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or \ (resid 60 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 61 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name ND2)) or (resid 62 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 63 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 64 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name NE \ 1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 65 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or nam \ e CD2 or name CE1 or name CE2 or name CZ )) or (resid 66 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2)) or (resid 67 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 68 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2 or name CD1)) or (resid 69 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (r \ esid 80 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name OD2)) or (resid 81 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2)) or (resid 82 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD )) or (resid 83 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 84 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 85 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 86 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or (resid 87 and (name N or name CA or name C or name O or name CB or name C \ G or name OD1 or name ND2)) or (resid 88 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name OD2)) or (resid 89 and (name N or \ name CA or name C or name O )) or (resid 90 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 91 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ or name OH )) or (resid 92 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or (resid 93 and (name N or name CA or name C or name O or name C \ B )) or (resid 94 and (name N or name CA or name C or name O or name CB or name \ OG )) or (resid 95 and (name N or name CA or name C or name O or name CB or name \ OG1 or name CG2)) or (resid 96 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name OE1 or name OE2)) or (resid 97 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name CE or nam \ e NZ )) or (resid 98 and (name N or name CA or name C or name O or name CB or na \ me OG )) or (resid 99 and (name N or name CA or name C or name O or name CB or n \ ame CG or name OD1 or name ND2)) or (resid 100 through 101 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid \ 102 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name NE or name CZ or name NH1 or name NH2)) or (resid 103 and (name N or na \ me CA or name C or name O )) or (resid 104 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or n \ ame CE3 or name CZ2 or name CZ3 or name CH2)) or (resid 105 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resi \ d 106 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 107 and (name N o \ r name CA or name C or name O )) or (resid 108 through 109 and (name N or name C \ A or name C or name O or name CB or name OG1 or name CG2)) or (resid 110 and (na \ me N or name CA or name C or name O or name CB or name CG or name CD1 or name CD \ 2)) or (resid 111 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name OD2)) or (resid 112 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 113 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 114 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 115 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name NE2)) or (resid 116 and (name N or name CA or name \ C or name O or name CB or name OG )) or (resid 117 through 118 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 119 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1)) or (resid 120 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 121 through 122 and (name N or name \ CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resi \ d 123 and (name N or name CA or name C or name O or name CB )) or (resid 124 and \ (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or \ (resid 125 and (name N or name CA or name C or name O or name CB or name CG or n \ ame OD1 or name ND2)) or (resid 126 through 127 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 128 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (re \ sid 129 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 130 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2)) or (resid 131 and (name N or name CA \ or name C or name O or name CB or name SG )) or (resid 132 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 133 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 134 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2)) or (resid 135 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) o \ r (resid 136 and (name N or name CA or name C or name O or name CB or name SG )) \ or (resid 137 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 138 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name OD2)) or (resid 139 and (name N or \ name CA or name C or name O or name CB or name CG or name CD )) or (resid 140 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD1 or na \ me CD2 or name CE1 or name CE2 or name CZ )) or (resid 141 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid \ 142 and (name N or name CA or name C or name O )) or (resid 143 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 165 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 166 and (name N or name CA or name C or name O or name CB or \ name SG )) or (resid 167 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2)) or (resid 168 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or (resid 169 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name OE2)) or (resid 170 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or \ name CE2 or name CZ or name OH )) or (resid 171 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 172 and (name N or nam \ e CA or name C or name O or name CB or name OG )) or (resid 186 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 187 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 188 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2)) or (resid 189 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2)) or (resid 190 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 191 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 192 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or (resid 193 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 194 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ )) or (resid 195 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ )) or (resid 196 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or (resid 197 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2 or name CD1)) or (resid 198 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name OD2)) or (resid 199 and (name \ N or name CA or name C or name O )) or (resid 200 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or (resid 201 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ )) or (resid 202 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE or name NZ )) or (resid 203 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid \ 204 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 205 and \ (name N or name CA or name C or name O or name CB or name OG )) or (resid 206 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ )) or (resid 207 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 2 \ 08 and (name N or name CA or name C or name O or name CB or name OG1 or name CG2 \ )) or (resid 209 and (name N or name CA or name C or name O or name CB or name C \ G or name CD )) or (resid 210 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name CD1)) or (resid 211 and (name N or name CA o \ r name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 212 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 213 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or (resid 214 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH \ 2)) or (resid 215 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name OD2)) or (resid 216 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2)) or (resid 217 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or (resid 218 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2)) or (resid 219 and (name N or name CA or name C or name O \ )) or (resid 220 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 221 an \ d (name N or name CA or name C or name O or name CB or name OG )) or (resid 222 \ and (name N or name CA or name C or name O or name CB )) or (resid 223 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2) \ ) or (resid 224 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or (resid 225 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or (resid 226 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or ( \ resid 227 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2)) or (resid 228 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 229 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 230 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD )) or (res \ id 231 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name CD1)) or (resid 232 and (name N or name CA or name C or name O )) o \ r (resid 233 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 234 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2)) or (resid 235 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or ( \ resid 236 and (name N or name CA or name C or name O or name CB or name OG1 or n \ ame CG2)) or (resid 237 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 23 \ 8 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ )) or (resid 239 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2)) or (resid 240 and (name N or name CA or name C or name 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name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 309 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 310 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name CE or name \ NZ )) or (resid 311 and (name N or name CA or name C or name O )) or (resid 312 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or \ name CD1)) or (resid 313 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH \ )) or (resid 314 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name NE2)) or (resid 315 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 316 and (name N \ or name CA or name C or name O or name CB or name OG )) or (resid 317 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or (resid 318 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 319 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2)) or (resid 320 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or (resid 321 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame NE2)) or (resid 322 and (name N or name CA or name C or name O or name CB or \ name CG or name CD )) or (resid 323 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2)) or (resid 324 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (res \ id 325 and (name N or name CA or name C or name O or name CB or name OG )) or (r \ esid 326 and (name N or name CA or name C or name O or name 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345 a \ nd (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) o \ r (resid 346 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 347 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ )) or (resid 348 and (name N or name CA or na \ me C or name O or name CB )) or (resid 349 and (name N or name CA or name C or n \ ame O or name CB or name OG )) or (resid 350 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 351 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ or name OH )) or (resid 352 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 353 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or na \ 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or name CG or name CD or name OE1 or name OE2)) or ( \ resid 466 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name NE or name CZ or name NH1 or name NH2)) or (resid 467 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) o \ r (resid 468 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 489 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ or name OH )) or (resid 490 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or \ (resid 491 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 492 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2)) or (resid 493 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resi \ d 494 and (name N or name CA or name C or name O or name CB or name OG )) or (re \ sid 495 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 496 \ and (name N or name CA or name C or name O )) or (resid 497 and (name N or name \ CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 \ or name CE2 or name CZ )) or (resid 498 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 499 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or ( \ resid 500 and (name N or name CA or name C or name O or name CB or name OG1 or n \ ame CG2)) or (resid 501 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2)) or (resid 503 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or (resid 504 and (name N or na \ me CA or name C or name O )) or (resid 505 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or n \ ame CZ or name OH )) or (resid 506 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2)) or (resid 507 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or (resid \ 508 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 509 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2)) or (resid 510 through 512 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 513 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 514 and (name N or name CA or name C or name O or name CB o \ r name OG )) or (resid 515 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (re \ sid 516 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2)) or (resid 517 through 518 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 519 \ and (name N or name CA or name C or name O or name CB or name CG or name ND1 or \ name CD2 or name CE1 or name NE2)) or (resid 520 and (name N or name CA or name \ C or name O or name CB )) or (resid 521 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD )) or (resid 522 and (name N or name CA or \ name C or name O or name CB )) or (resid 523 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 524 and (name N or name C \ A or name C or name O or name CB or name CG1 or name CG2)) or (resid 525 and (na \ me N or name CA or name C or name O or name CB or name SG )) or (resid 526 and ( \ name N or name CA or name C or name O )) or (resid 527 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or (resid 528 through 529 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame CE or name NZ )) or (resid 530 and (name N or name CA or name C or name O or \ name CB or name OG )) or (resid 531 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2)) or (resid 532 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 533 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 534 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2)) or (resid 535 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ )) or (resid 536 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or (resid 537 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 538 and (name N or name CA or name \ C or name O or name CB or name SG )) or (resid 539 and (name N or name CA or na \ me C or name O or name CB or name CG1 or name CG2)) or (resid 540 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or \ (resid 541 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 542 and (nam \ e N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 \ )) or (resid 543 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 544 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 545 and (name N or name CA or name C or name O )) or (resid 5 \ 46 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 547 and (name N or name CA or name C or name O or name C \ B or name OG1 or name CG2)) or (resid 548 and (name N or name CA or name C or na \ me O )) or (resid 549 and (name N or name CA or name C or name O or name CB or n \ ame OG1 or name CG2)) or (resid 550 and (name N or name CA or name C or name O ) \ ) or (resid 551 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or (resid 552 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 553 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 554 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or \ name OE2)) or (resid 555 and (name N or name CA or name C or name O or name CB o \ r name OG )) or (resid 556 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2)) or (resid 557 through 558 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE or name N \ Z )) or (resid 559 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 560 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 561 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 562 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name C \ Z )) or (resid 563 through 564 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name NE2)) or (resid 565 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or n \ ame CE1 or name CE2 or name CZ )) or (resid 566 and (name N or name CA or name C \ or name O )) or (resid 567 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resi \ d 568 and (name N or name CA or name C or name O or name CB or name CG or name O \ D1 or name OD2)) or (resid 569 and (name N or name CA or name C or name O or nam \ e CB or name CG1 or name CG2 or name CD1)) or (resid 570 and (name N or name CA \ or name C or name O or name CB )) or (resid 571 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2)) or (resid 572 through \ 573 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2)) or (resid 574 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name OD2)) or (resid 575 and (name N or name CA or name C or \ name O or name CB )) or (resid 576 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 577 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or (resid 578 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name OD2)) or (resid 579 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or (resid 580 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ NE2)) or (resid 581 and (name N or name CA or name C or name O or name CB or na \ me OG1 or name CG2)) or (resid 582 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 583 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2) \ ) or (resid 584 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2 or name CD1)) or (resid 585 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2)) or (resid 586 and (name N o \ r name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or \ (resid 587 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2 or name CD1)) or (resid 588 and (name N or name CA or name C or name O \ or name CB or name OG1 or name CG2)) or (resid 589 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or (resid 590 and (name N or \ name CA or name C or name O or name CB or name SG )) or (resid 591 and (name N o \ r name CA or name C or name O or name CB or name OG )) or (resid 592 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or (resid 593 through 594 and (name N or nam \ e CA or name C or name O )) or (resid 595 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2)) or (resid 596 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 597 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 598 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD \ 1)) or (resid 599 and (name N or name CA or name C or name O or name CB or name \ OG1 or name CG2)) or (resid 600 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or (resid 601 and (name N or name CA or name C or \ name O )) or (resid 602 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2)) or (resid 603 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2)) or (resid 604 and (name N or n \ ame CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 605 an \ d (name N or name CA or name C or name O or name CB or name OG )) or (resid 606 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2)) or (resid 607 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2)) or (resid 608 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 609 and ( \ name N or name CA or name C or name O or name CB )) or (resid 610 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 611 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 612 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH \ )) or (resid 613 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name NE2)) or (resid 614 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 615 an \ d (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 616 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name ND2)) or (resid 617 and (name N or name CA or name C or name O \ or name CB or name SG )) or (resid 618 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2)) or (resid 619 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (r \ esid 620 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2)) or (resid 641 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name ND2)) or (resid 642 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 643 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ )) or (resid 644 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 645 a \ nd (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) o \ r (resid 646 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 647 and (name \ N or name CA or name C or name O or name CB )) or (resid 648 and (name N or nam \ e CA or name C or name O )) or (resid 649 and (name N or name CA or name C or na \ me O or name CB or name SG )) or (resid 650 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 651 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) \ or (resid 652 and (name N or name CA or name C or name O )) or (resid 653 and ( \ name N or name CA or name C or name O or name CB )) or (resid 654 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 655 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 656 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 657 through 658 and (name N or name CA or name C or name O or name CB or name C \ G or name OD1 or name ND2)) or (resid 659 and (name N or name CA or name C or na \ me O or name CB or name OG )) or (resid 660 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name OH )) or (resid 661 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name OE2)) or (resid 662 and (nam \ e N or name CA or name C or name O or name CB or name SG )) or (resid 663 and (n \ ame N or name CA or name C or name O or name CB or name CG or name OD1 or name O \ D2)) or (resid 664 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2 or name CD1)) or (resid 665 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or (resid 666 and (name N or name CA \ or name C or 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(name N or name CA or name C or name O or name CB or name \ OG )) or (resid 690 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name NE2)) or (resid 691 and (name N or name CA o \ r name C or name O or name CB or name OG )) or (resid 692 through 693 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1) \ ) or (resid 694 and (name N or name CA or name C or name O or name CB )) or (res \ id 695 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 696 a \ nd (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) o \ r (resid 697 and (name N or name CA or name C or name O or name CB or name CG or \ name SD or name CE )) or (resid 698 and (name N or name CA or name C or name O \ or name CB or name OG )) or (resid 699 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or (resid 700 and (name N or n \ ame CA or name C or name O )) or (resid 701 and (name N or name CA or name C or \ name O or name CB )) or (resid 702 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 703 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name ND2) \ ) or (resid 704 and (name N or name CA or name C or name O or name CB or name OG \ )) or (resid 705 and (name N or name CA or name C or name O or name CB or name \ CG1 or name CG2)) or (resid 706 and (name N or name CA or name C or name O or na \ me CB )) or (resid 707 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) \ or (resid 708 and (name N or name CA or name C or name O or name CB or name OG \ )) or (resid 709 through 710 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2)) or (resid 711 and (name N or name CA or \ name C or name O or name CB or name OG )) or (resid 712 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 71 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 714 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 715 and (name N or name CA or name C or name O or name CB or name \ CG or name CD )) or (resid 716 and (name N or name CA or name C or name O or na \ me CB or name OG1 or name CG2)) or (resid 717 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2)) or (resid 718 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ )) or (resid 719 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2)) or (resid 720 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or \ (resid 721 and (name N or name CA or name C or name O or name CB or name OG )) \ or (resid 722 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or (resid 723 through 724 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2)) or (resid 725 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or ( \ resid 726 and (name N or name CA or name C or name O or name CB or name CG1 or n \ ame CG2 or name CD1)) or (resid 727 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD1 or name CD2)) or (resid 728 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 729 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 730 and (name N or name CA or name C or name O or name CB or name OG )) or ( \ resid 731 and (name N or name CA or name C or name O or name 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OG1 or name CG2)) or (resid 867 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 868 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE \ 2)) or (resid 869 and (name N or name CA or name C or name O or name CB or name \ CG or name SD or name CE )) or (resid 870 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2 or name CD1)) or (resid 871 and (name N \ or name CA or name C or name O or name CB )) or (resid 872 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name NE2)) \ or (resid 873 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (res \ id 874 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 875 and (name N or name CA or name C or name O or name CB or na \ me OG )) or 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name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 888 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 889 and (name \ N or name CA or name C or name O )) or (resid 890 and (name N or name CA or name \ C or name O or name CB )) or (resid 891 and (name N or name CA or name C or nam \ e O )) or (resid 892 through 893 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 894 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2)) or (resid 895 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid \ 896 and (name N or name CA or name C or name O or name CB or name CG1 or name C \ G2 or name CD1)) or (resid 897 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD )) or (resid 898 and (name N or name CA or name C or \ name O or name CB or name CG or 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and (name N or name CA or name C or na \ me O or name CB or name CG or name OD1 or name ND2)) or (resid 908 and (name N o \ r name CA or name C or name O )) or (resid 909 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 910 and (na \ me N or name CA or name C or name O )) or (resid 911 and (name N or name CA or n \ ame C or name O or name CB or name CG1 or name CG2)) or (resid 912 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 913 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2)) or (resid 914 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name ND2)) or (resid 915 and (name N or nam \ e CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 916 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 917 and (name N or name CA or name 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N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (re \ sid 927 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 928 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) \ or (resid 929 and (name N or name CA or name C or name O or name CB or name OG ) \ ) or (resid 930 and (name N or name CA or name C or name O or name CB )) or (res \ id 931 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name CD1)) or (resid 932 and (name N or name CA or name C or name O )) o \ r (resid 933 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE or name NZ )) or (resid 934 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 935 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or 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CG or name CD or name CE or name NZ )) or (resid 948 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 949 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me OE1 or name NE2)) or (resid 950 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 951 through 952 and (nam \ e N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resi \ d 953 and (name N or name CA or name C or name O or name CB or name CG or name O \ D1 or name ND2)) or (resid 954 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name OE1 or name NE2)) or (resid 955 and (name N o \ r name CA or name C or name O or name CB or name CG or name OD1 or name ND2)) or \ (resid 956 and (name N or name CA or name C or name O or name CB )) or (resid 9 \ 57 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2)) or (resid 958 and (name N or name CA or name C or name \ O or name CB )) or (resid 959 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2)) or (resid 960 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 961 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 962 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2)) or (resid 963 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 964 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name CE or name NZ )) or (re \ sid 965 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 966 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2)) or (resid 967 through 968 \ and (name N or name CA or name C or name O or name CB or name OG )) or (resid 9 \ 69 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name ND2)) or (resid 970 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (r \ esid 971 and (name N or name CA or name C or name O )) or (resid 972 and (name N \ or name CA or name C or name O or name CB )) or (resid 973 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resi \ d 974 through 975 and (name N or name CA or name C or name O or name CB or name \ OG )) or (resid 976 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2)) or (resid 977 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 978 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid \ 979 and (name N or name CA or 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name CB or name OG1 or nam \ e CG2)) or (resid 999 and (name N or name CA or name C or name O )) or (resid 10 \ 00 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE or name CZ or name NH1 or name NH2)) or (resid 1001 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (res \ id 1002 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 1003 and (name N or name CA or name C or \ name O or name CB or name OG )) or (resid 1004 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)) or (resid 1005 and (n \ ame N or name CA or name C or name O or name CB or name CG or name CD or name OE \ 1 or name NE2)) or (resid 1006 and (name N or name CA or name C or name O or nam \ e CB or name OG1 or name CG2)) or (resid 1007 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 o \ r name CZ or name OH )) or (resid 1008 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 1009 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 1010 through 101 \ 1 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2)) or (resid 1012 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2)) or (resid 1013 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or \ (resid 1014 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 1015 through 1 \ 016 and (name N or name CA or name C or name O or name CB )) or (resid 1017 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name OE2)) or (resid 1018 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2 or name CD1)) or (resid 1019 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ or \ name NH1 or name NH2)) or (resid 1020 and (name N or name CA or name C or name \ O or name CB )) or (resid 1021 and (name N or name CA or name C or name O or nam \ e CB or name OG )) or (resid 1022 and (name N or name CA or name C or name O or \ name CB )) or (resid 1023 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2)) or (resid 1024 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 1025 th \ rough 1026 and (name N or name CA or name C or name O or name CB )) or (resid 10 \ 27 and (name N or name CA or name C or name O or name CB or name OG1 or name CG2 \ )) or (resid 1028 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ )) or (resid 1029 and (name N or name CA or \ name C or name O or name CB or name CG or name SD or name CE )) or (resid 1030 a \ nd (name N or name CA or name C or name O or name CB or name OG )) or (resid 103 \ 1 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name OE2)) or (resid 1032 and (name N or name CA or name C or name \ O or name CB or name SG )) or (resid 1033 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2)) or (resid 1034 and (name N or name CA \ or name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 10 \ 35 and (name N or name CA or name C or name O )) or (resid 1036 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ NE2)) or (resid 1037 and (name N or name CA or name C or name O or name CB or na \ me OG )) or (resid 1038 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE or name NZ )) or (resid 1039 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE or name CZ or \ name NH1 or name NH2)) or (resid 1040 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 1041 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 1042 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 1043 and (name N or nam \ e CA or name C or name O or name CB or name SG )) or (resid 1044 and (name N or \ name CA or name C or name O )) or (resid 1045 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE or name NZ )) or (resid 104 \ 6 and (name N or name CA or name C or name O )) or (resid 1047 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ or name OH )) or (resid 1048 and (name N or name CA o \ r name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2)) or (resid 1049 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2)) or (resid 1050 and (name N or name CA or na \ me C or name O or name CB or name CG or name SD or name CE )) or (resid 1051 and \ (name N or name CA or name C or name O or name CB or name OG )) or (resid 1052 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ )) or (resid 1053 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or (resid 1054 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ OE1 or name NE2)) or (resid 1055 and (name N or name CA or name C or name O or n \ ame CB or name OG )) or (resid 1056 and (name N or name CA or name C or name O o \ r name CB )) or (resid 1057 and (name N or name CA or name C or name O or name C \ B or name CG or name CD )) or (resid 1058 and (name N or name CA or name C or na \ me O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or \ (resid 1059 and (name N or name CA or name C or name O )) or (resid 1060 through \ 1061 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2)) or (resid 1062 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 10 \ 63 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2)) or (resid 1064 and (name N or name CA or name C or name O or name \ CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 1065 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r (resid 1066 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 1067 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name \ OH )) or (resid 1068 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2)) or (resid 1069 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or (resid 1070 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 1071 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 1072 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name OE2)) or (resid 1073 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name CE or name NZ )) or (resid 1074 and (na \ me N or name CA or name C or name O or name CB or name CG or name OD1 or name ND \ 2)) or (resid 1075 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 1076 \ through 1077 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 1078 and (name N or name CA or name C or name O or name \ CB )) or (resid 1079 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or (resid 1080 and (name N or name CA or name C or name O or \ name CB )) or (resid 1081 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1)) or (resid 1082 and (name N or name CA or \ name C or name O or name CB or name SG )) or (resid 1083 and (name N or name CA \ or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or \ name NE2)) or (resid 1084 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name OD2)) or (resid 1085 and (name N or name CA or n \ ame C or name O )) or (resid 1086 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ )) or (resid 1087 and (name \ N or name CA or name C or name O or name CB )) or (resid 1088 and (name N or nam \ e CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name C \ E1 or name NE2)) or (resid 1089 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) o \ r (resid 1090 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD )) or (resid 1091 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resi \ d 1092 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name OE2)) or (resid 1093 and (name N or name CA or name C or \ name O )) or (resid 1094 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or (resid 1095 and (name N or name CA or name C or name \ O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or (resid 1096 and (name N or name CA or name C or name O or name CB or n \ ame CG1 or name CG2)) or (resid 1097 and (name N or name CA or name C or name O \ or name CB or name OG )) or (resid 1098 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name ND2)) or (resid 1099 and (name N or \ name CA or name C or name O )) or (resid 1100 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 1101 and (name N or nam \ e CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name C \ E1 or name NE2)) or (resid 1102 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name NE1 or name CE2 or name CE3 or \ name CZ2 or name CZ3 or name CH2)) or (resid 1103 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or (resid 1104 and (name N or name CA or name C or name O or na \ me CB or name CG1 or name CG2)) or (resid 1105 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 1106 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name OE1 or name NE \ 2)) or (resid 1107 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 1108 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me ND2)) or (resid 1109 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid \ 1110 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 1111 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me OE1 or name OE2)) or (resid 1112 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or (resid 1113 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or (resi \ d 1114 through 1115 and (name N or name CA or name C or name O or name CB or nam \ e CG1 or name CG2 or name CD1)) or (resid 1116 through 1117 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 1118 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2)) or (resid 1119 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name ND2)) or (resid 1120 and (name N or name CA or name C \ or name O or name CB or name OG1 or name CG2)) or (resid 1121 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ )) or (resid 1122 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 1123 and (name N or name C \ A or name C or name O or name CB or name OG )) or (resid 1124 and (name N or nam \ e CA or name C or name O )) or (resid 1125 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2)) or (resid 1126 and (name N \ or name CA or name C or name O or name CB or name SG )) or (resid 1127 and (nam \ e N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2 \ )) or (resid 1128 through 1129 and (name N or name CA or name C or name O or nam \ e CB or name CG1 or name CG2)) or (resid 1130 and (name N or name CA or name C o \ r name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 1131 and (na \ me N or name CA or name C or name O )) or (resid 1132 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 1133 \ and (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) \ or (resid 1134 through 1135 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2)) or (resid 1136 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 1137 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid \ 1138 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 1139 an \ d (name N or name CA or name C or name O or name CB or name CG or name OD1 or na \ me OD2)) or (resid 1140 and (name N or name CA or name C or name O or name CB or \ name CG or name CD )) or (resid 1141 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 1142 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ NE2)) or (resid 1143 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or (resid 1144 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name OE2)) or (resid 1145 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ )) or (resid 1146 and (name N or name CA or name C or name O or name CB or name \ CG or name OD1 or name OD2)) or (resid 1147 and (name N or name CA or name C or \ name O or name CB or name OG )) or resid 1301 through 1310)) selection = (chain 'B' and resid 27 through 1210) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'E' and resid 1 through 4) selection = (chain 'T' and resid 1 through 4) } ncs_group { reference = (chain 'H' and (resid 1 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB or name SG or name H or name HA or name HB2 or name HB3)) \ or resid 23 through 91 or (resid 92 and (name N or name CA or name C or name O o \ r name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 93 \ through 141 or (resid 142 and (name N or name CA or name C or name O or name CB \ or name SG or name H or name HA or name HB2 or name HB3)) or resid 143 through 2 \ 07 or (resid 208 and (name N or name CA or name C or name O or name CB or name S \ G or name H or name HA or name HB2 or name HB3)) or resid 209 through 228)) selection = chain 'M' } ncs_group { reference = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 3 through 212)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.290 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 45.490 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.015 0.500 31034 Z= 0.858 Angle : 1.636 50.299 42351 Z= 1.072 Chirality : 0.103 2.322 5014 Planarity : 0.013 0.289 5314 Dihedral : 13.227 111.336 12115 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.70 % Allowed : 2.22 % Favored : 97.08 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 3692 helix: -0.65 (0.17), residues: 713 sheet: 0.30 (0.16), residues: 952 loop : -0.10 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 108 TYR 0.158 0.009 TYR A 37 PHE 0.077 0.006 PHE A 220 TRP 0.152 0.013 TRP H 157 HIS 0.014 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.01481 (30921) covalent geometry : angle 1.54729 (42056) SS BOND : bond 0.05357 ( 44) SS BOND : angle 8.79286 ( 88) hydrogen bonds : bond 0.17889 ( 1266) hydrogen bonds : angle 8.86398 ( 3651) link_ALPHA1-2 : bond 0.01427 ( 1) link_ALPHA1-2 : angle 4.42306 ( 3) link_ALPHA1-3 : bond 0.00646 ( 2) link_ALPHA1-3 : angle 2.22492 ( 6) link_ALPHA1-6 : bond 0.01297 ( 3) link_ALPHA1-6 : angle 3.02154 ( 9) link_BETA1-3 : bond 0.02520 ( 2) link_BETA1-3 : angle 4.17083 ( 6) link_BETA1-4 : bond 0.05066 ( 16) link_BETA1-4 : angle 3.14739 ( 48) link_BETA1-6 : bond 0.00004 ( 1) link_BETA1-6 : angle 0.98161 ( 3) link_NAG-ASN : bond 0.10438 ( 44) link_NAG-ASN : angle 6.20576 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 436 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6302 (m-90) cc_final: 0.5763 (m-90) REVERT: A 194 PHE cc_start: 0.7480 (m-80) cc_final: 0.6824 (m-10) REVERT: A 351 TYR cc_start: 0.8010 (p90) cc_final: 0.7764 (p90) REVERT: A 451 TYR cc_start: 0.3328 (m-80) cc_final: 0.2800 (m-80) REVERT: A 571 ASP cc_start: 0.7587 (t0) cc_final: 0.7046 (t0) REVERT: B 189 LEU cc_start: 0.8748 (tp) cc_final: 0.8018 (tp) REVERT: B 223 LEU cc_start: 0.7117 (mp) cc_final: 0.6865 (tp) REVERT: B 369 TYR cc_start: 0.8703 (t80) cc_final: 0.8250 (t80) REVERT: B 387 LEU cc_start: 0.9017 (mt) cc_final: 0.8651 (mt) REVERT: B 437 ASN cc_start: 0.8100 (p0) cc_final: 0.7272 (p0) REVERT: B 745 ASP cc_start: 0.6602 (m-30) cc_final: 0.6122 (p0) REVERT: B 979 ASP cc_start: 0.8611 (m-30) cc_final: 0.8260 (t0) REVERT: C 384 PRO cc_start: 0.8562 (Cg_endo) cc_final: 0.8010 (Cg_exo) REVERT: C 417 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8978 (tptt) REVERT: C 424 LYS cc_start: 0.7429 (tptt) cc_final: 0.6965 (ttmt) REVERT: C 513 LEU cc_start: 0.8583 (mt) cc_final: 0.8317 (mt) REVERT: C 564 GLN cc_start: 0.7981 (tp40) cc_final: 0.7741 (tp-100) REVERT: C 571 ASP cc_start: 0.7685 (t0) cc_final: 0.7480 (t0) REVERT: C 1128 VAL cc_start: 0.7099 (t) cc_final: 0.6825 (p) REVERT: H 178 LEU cc_start: 0.8956 (tp) cc_final: 0.8685 (tp) REVERT: L 4 MET cc_start: 0.6311 (mtm) cc_final: 0.5861 (mtm) REVERT: M 35 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7177 (m-40) REVERT: M 70 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7531 (m) REVERT: M 76 ASP cc_start: 0.8088 (m-30) cc_final: 0.7887 (m-30) REVERT: M 83 ARG cc_start: 0.8475 (mtt180) cc_final: 0.8148 (mmp80) outliers start: 23 outliers final: 7 residues processed: 457 average time/residue: 0.3921 time to fit residues: 265.8127 Evaluate side-chains 239 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 229 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 35 ASN Chi-restraints excluded: chain M residue 70 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 603 ASN A 762 GLN A1005 GLN B 125 ASN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 907 ASN B 935 GLN B 955 ASN B1010 GLN B1088 HIS C 125 ASN C 519 HIS C 613 GLN C 804 GLN C 935 GLN C 955 ASN C 957 GLN C1002 GLN C1010 GLN C1088 HIS K 38 GLN M 81 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.083787 restraints weight = 180520.474| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.08 r_work: 0.3492 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 31034 Z= 0.160 Angle : 0.673 24.782 42351 Z= 0.348 Chirality : 0.046 0.720 5014 Planarity : 0.004 0.132 5314 Dihedral : 9.000 81.460 5463 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.40 % Allowed : 5.65 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 3692 helix: 0.99 (0.19), residues: 702 sheet: 0.30 (0.15), residues: 1039 loop : 0.01 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 142 TYR 0.019 0.001 TYR A1067 PHE 0.023 0.001 PHE K 83 TRP 0.013 0.001 TRP H 157 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00346 (30921) covalent geometry : angle 0.62930 (42056) SS BOND : bond 0.00822 ( 44) SS BOND : angle 2.43246 ( 88) hydrogen bonds : bond 0.05165 ( 1266) hydrogen bonds : angle 6.58229 ( 3651) link_ALPHA1-2 : bond 0.00258 ( 1) link_ALPHA1-2 : angle 1.74571 ( 3) link_ALPHA1-3 : bond 0.00684 ( 2) link_ALPHA1-3 : angle 2.29654 ( 6) link_ALPHA1-6 : bond 0.00778 ( 3) link_ALPHA1-6 : angle 1.79652 ( 9) link_BETA1-3 : bond 0.00422 ( 2) link_BETA1-3 : angle 3.30707 ( 6) link_BETA1-4 : bond 0.00512 ( 16) link_BETA1-4 : angle 2.24343 ( 48) link_BETA1-6 : bond 0.00013 ( 1) link_BETA1-6 : angle 2.85552 ( 3) link_NAG-ASN : bond 0.00636 ( 44) link_NAG-ASN : angle 3.46827 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.7756 (t0) cc_final: 0.7073 (t0) REVERT: A 697 MET cc_start: 0.8247 (ptm) cc_final: 0.8042 (ptp) REVERT: B 223 LEU cc_start: 0.7485 (mp) cc_final: 0.7174 (tp) REVERT: B 369 TYR cc_start: 0.8843 (t80) cc_final: 0.8342 (t80) REVERT: B 964 LYS cc_start: 0.9359 (mttt) cc_final: 0.9095 (mttp) REVERT: B 979 ASP cc_start: 0.8865 (m-30) cc_final: 0.8660 (t0) REVERT: C 135 PHE cc_start: 0.8192 (m-80) cc_final: 0.7893 (m-10) REVERT: C 378 LYS cc_start: 0.8320 (tppt) cc_final: 0.7973 (tptt) REVERT: C 417 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8921 (tptt) REVERT: C 564 GLN cc_start: 0.8070 (tp40) cc_final: 0.7835 (tp-100) REVERT: C 571 ASP cc_start: 0.7993 (t0) cc_final: 0.7700 (t70) REVERT: H 72 ASP cc_start: 0.7458 (t0) cc_final: 0.7144 (t0) REVERT: H 82 MET cc_start: 0.8195 (mtp) cc_final: 0.7920 (mtp) REVERT: K 173 TYR cc_start: 0.6948 (m-80) cc_final: 0.6421 (m-80) REVERT: L 4 MET cc_start: 0.6026 (mtm) cc_final: 0.5694 (mtm) outliers start: 46 outliers final: 26 residues processed: 280 average time/residue: 0.3937 time to fit residues: 162.0682 Evaluate side-chains 218 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 210 ASN Chi-restraints excluded: chain L residue 29 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 83 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 270 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 804 GLN A 914 ASN A 935 GLN A1005 GLN B 207 HIS B 317 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 66 HIS C 955 ASN H 209 ASN K 137 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.080778 restraints weight = 178587.742| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.81 r_work: 0.3288 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 31034 Z= 0.271 Angle : 0.690 19.976 42351 Z= 0.355 Chirality : 0.047 0.631 5014 Planarity : 0.005 0.051 5314 Dihedral : 6.895 70.178 5457 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.64 % Allowed : 7.20 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 3692 helix: 0.73 (0.19), residues: 717 sheet: -0.00 (0.16), residues: 1012 loop : -0.29 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 142 TYR 0.026 0.002 TYR C 789 PHE 0.027 0.002 PHE C1089 TRP 0.016 0.001 TRP B1102 HIS 0.006 0.001 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00609 (30921) covalent geometry : angle 0.66089 (42056) SS BOND : bond 0.00776 ( 44) SS BOND : angle 1.99876 ( 88) hydrogen bonds : bond 0.04605 ( 1266) hydrogen bonds : angle 6.21913 ( 3651) link_ALPHA1-2 : bond 0.00511 ( 1) link_ALPHA1-2 : angle 2.55341 ( 3) link_ALPHA1-3 : bond 0.00926 ( 2) link_ALPHA1-3 : angle 2.68555 ( 6) link_ALPHA1-6 : bond 0.00743 ( 3) link_ALPHA1-6 : angle 2.71274 ( 9) link_BETA1-3 : bond 0.00171 ( 2) link_BETA1-3 : angle 2.69491 ( 6) link_BETA1-4 : bond 0.00436 ( 16) link_BETA1-4 : angle 1.69247 ( 48) link_BETA1-6 : bond 0.00313 ( 1) link_BETA1-6 : angle 2.22064 ( 3) link_NAG-ASN : bond 0.00660 ( 44) link_NAG-ASN : angle 2.89310 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 LYS cc_start: 0.8740 (pttt) cc_final: 0.8160 (pttt) REVERT: A 204 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7152 (m-80) REVERT: A 359 SER cc_start: 0.7877 (p) cc_final: 0.7657 (m) REVERT: A 394 ASN cc_start: 0.6452 (m-40) cc_final: 0.5759 (m-40) REVERT: A 571 ASP cc_start: 0.7969 (t0) cc_final: 0.7385 (t0) REVERT: B 52 GLN cc_start: 0.8890 (tt0) cc_final: 0.8097 (tm-30) REVERT: B 195 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8259 (ptpt) REVERT: B 369 TYR cc_start: 0.8783 (t80) cc_final: 0.8424 (t80) REVERT: C 52 GLN cc_start: 0.8217 (tt0) cc_final: 0.7677 (tm-30) REVERT: C 135 PHE cc_start: 0.8203 (m-80) cc_final: 0.7961 (m-10) REVERT: C 351 TYR cc_start: 0.7902 (p90) cc_final: 0.7652 (p90) REVERT: C 380 TYR cc_start: 0.7956 (m-10) cc_final: 0.7562 (m-10) REVERT: C 417 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8974 (tttt) REVERT: C 564 GLN cc_start: 0.8332 (tp40) cc_final: 0.8045 (tp-100) REVERT: C 571 ASP cc_start: 0.8051 (t0) cc_final: 0.7806 (t70) REVERT: C 869 MET cc_start: 0.9023 (mtt) cc_final: 0.8476 (mtt) REVERT: C 985 ASP cc_start: 0.8342 (p0) cc_final: 0.7143 (p0) REVERT: H 72 ASP cc_start: 0.7575 (t0) cc_final: 0.7342 (t70) REVERT: H 82 MET cc_start: 0.8279 (mtp) cc_final: 0.8007 (mtp) REVERT: H 91 TYR cc_start: 0.5394 (OUTLIER) cc_final: 0.4720 (m-80) REVERT: L 4 MET cc_start: 0.6327 (mtm) cc_final: 0.5979 (mtm) REVERT: L 123 GLU cc_start: 0.7647 (pt0) cc_final: 0.7087 (pm20) REVERT: M 82 MET cc_start: 0.8366 (mtt) cc_final: 0.7790 (mmm) REVERT: M 218 LYS cc_start: 0.8330 (mttt) cc_final: 0.7913 (tptt) REVERT: M 228 LYS cc_start: 0.5644 (ttmt) cc_final: 0.5217 (pttm) outliers start: 54 outliers final: 38 residues processed: 251 average time/residue: 0.3961 time to fit residues: 147.9852 Evaluate side-chains 221 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 207 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 339 optimal weight: 0.5980 chunk 103 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 238 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.129116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.077194 restraints weight = 178673.872| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.19 r_work: 0.3330 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 31034 Z= 0.161 Angle : 0.561 18.200 42351 Z= 0.288 Chirality : 0.044 0.553 5014 Planarity : 0.004 0.052 5314 Dihedral : 6.169 57.223 5457 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.40 % Allowed : 8.63 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3692 helix: 1.19 (0.20), residues: 735 sheet: -0.08 (0.16), residues: 1032 loop : -0.22 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.020 0.001 TYR M 185 PHE 0.020 0.001 PHE C 201 TRP 0.008 0.001 TRP H 157 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00359 (30921) covalent geometry : angle 0.52956 (42056) SS BOND : bond 0.00446 ( 44) SS BOND : angle 2.21702 ( 88) hydrogen bonds : bond 0.03901 ( 1266) hydrogen bonds : angle 5.85438 ( 3651) link_ALPHA1-2 : bond 0.00230 ( 1) link_ALPHA1-2 : angle 1.91471 ( 3) link_ALPHA1-3 : bond 0.00921 ( 2) link_ALPHA1-3 : angle 2.55323 ( 6) link_ALPHA1-6 : bond 0.00327 ( 3) link_ALPHA1-6 : angle 1.73816 ( 9) link_BETA1-3 : bond 0.00289 ( 2) link_BETA1-3 : angle 2.36777 ( 6) link_BETA1-4 : bond 0.00418 ( 16) link_BETA1-4 : angle 1.46916 ( 48) link_BETA1-6 : bond 0.00579 ( 1) link_BETA1-6 : angle 1.86973 ( 3) link_NAG-ASN : bond 0.00380 ( 44) link_NAG-ASN : angle 2.56032 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7123 (mmt180) REVERT: A 359 SER cc_start: 0.7817 (p) cc_final: 0.7561 (m) REVERT: A 378 LYS cc_start: 0.8111 (tptp) cc_final: 0.7875 (tptp) REVERT: A 394 ASN cc_start: 0.6435 (m-40) cc_final: 0.5747 (m-40) REVERT: A 417 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8300 (tptp) REVERT: A 571 ASP cc_start: 0.7912 (t0) cc_final: 0.7335 (t0) REVERT: A 780 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8446 (pt0) REVERT: B 52 GLN cc_start: 0.8832 (tt0) cc_final: 0.8014 (tm-30) REVERT: B 195 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8109 (pttm) REVERT: B 270 LEU cc_start: 0.7940 (mt) cc_final: 0.7729 (mt) REVERT: B 369 TYR cc_start: 0.8847 (t80) cc_final: 0.8340 (t80) REVERT: B 985 ASP cc_start: 0.8223 (p0) cc_final: 0.7540 (p0) REVERT: B 1092 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: C 52 GLN cc_start: 0.8274 (tt0) cc_final: 0.7700 (tm-30) REVERT: C 135 PHE cc_start: 0.8324 (m-80) cc_final: 0.8055 (m-10) REVERT: C 351 TYR cc_start: 0.8034 (p90) cc_final: 0.7749 (p90) REVERT: C 380 TYR cc_start: 0.7853 (m-10) cc_final: 0.7482 (m-10) REVERT: C 417 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8993 (tttt) REVERT: C 424 LYS cc_start: 0.8311 (tptt) cc_final: 0.7543 (ttmt) REVERT: C 564 GLN cc_start: 0.8332 (tp40) cc_final: 0.8117 (tp-100) REVERT: C 571 ASP cc_start: 0.8082 (t0) cc_final: 0.7832 (t70) REVERT: C 869 MET cc_start: 0.8929 (mtt) cc_final: 0.8305 (mtt) REVERT: C 960 ASN cc_start: 0.9013 (m-40) cc_final: 0.8763 (t0) REVERT: H 91 TYR cc_start: 0.5508 (OUTLIER) cc_final: 0.4777 (m-80) REVERT: L 4 MET cc_start: 0.6269 (mtm) cc_final: 0.6021 (mtm) REVERT: L 123 GLU cc_start: 0.7667 (pt0) cc_final: 0.7099 (pm20) REVERT: M 82 MET cc_start: 0.8386 (mtt) cc_final: 0.7781 (mmm) REVERT: M 218 LYS cc_start: 0.8344 (mttt) cc_final: 0.7947 (tptt) outliers start: 46 outliers final: 34 residues processed: 226 average time/residue: 0.3874 time to fit residues: 130.6387 Evaluate side-chains 214 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 82 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 260 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 37 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 340 optimal weight: 30.0000 chunk 270 optimal weight: 8.9990 chunk 371 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1119 ASN C 493 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.124520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.075897 restraints weight = 176600.833| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.49 r_work: 0.3267 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 31034 Z= 0.244 Angle : 0.623 17.237 42351 Z= 0.317 Chirality : 0.045 0.518 5014 Planarity : 0.004 0.050 5314 Dihedral : 5.979 59.125 5457 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.85 % Allowed : 9.09 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3692 helix: 0.97 (0.19), residues: 741 sheet: -0.29 (0.15), residues: 1033 loop : -0.42 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1107 TYR 0.040 0.002 TYR K 173 PHE 0.020 0.002 PHE B1103 TRP 0.010 0.001 TRP A1102 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00549 (30921) covalent geometry : angle 0.59638 (42056) SS BOND : bond 0.00408 ( 44) SS BOND : angle 1.88895 ( 88) hydrogen bonds : bond 0.03997 ( 1266) hydrogen bonds : angle 5.86338 ( 3651) link_ALPHA1-2 : bond 0.00530 ( 1) link_ALPHA1-2 : angle 2.50927 ( 3) link_ALPHA1-3 : bond 0.00606 ( 2) link_ALPHA1-3 : angle 2.77794 ( 6) link_ALPHA1-6 : bond 0.00458 ( 3) link_ALPHA1-6 : angle 2.38107 ( 9) link_BETA1-3 : bond 0.00170 ( 2) link_BETA1-3 : angle 2.53359 ( 6) link_BETA1-4 : bond 0.00292 ( 16) link_BETA1-4 : angle 1.41347 ( 48) link_BETA1-6 : bond 0.00558 ( 1) link_BETA1-6 : angle 1.89989 ( 3) link_NAG-ASN : bond 0.00457 ( 44) link_NAG-ASN : angle 2.60020 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 188 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7094 (mmt180) REVERT: A 195 LYS cc_start: 0.8715 (pttt) cc_final: 0.8334 (pttt) REVERT: A 204 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: A 571 ASP cc_start: 0.7909 (t0) cc_final: 0.7386 (t0) REVERT: A 780 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: B 52 GLN cc_start: 0.8842 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 204 TYR cc_start: 0.7948 (m-80) cc_final: 0.7419 (m-80) REVERT: B 270 LEU cc_start: 0.8187 (mt) cc_final: 0.7967 (mt) REVERT: B 369 TYR cc_start: 0.8967 (t80) cc_final: 0.8743 (t80) REVERT: B 370 ASN cc_start: 0.8792 (m-40) cc_final: 0.8571 (p0) REVERT: B 740 MET cc_start: 0.9007 (ttt) cc_final: 0.8684 (mtp) REVERT: B 1092 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: C 52 GLN cc_start: 0.8406 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 135 PHE cc_start: 0.8353 (m-80) cc_final: 0.8024 (m-10) REVERT: C 191 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7904 (mp0) REVERT: C 351 TYR cc_start: 0.8010 (p90) cc_final: 0.7706 (p90) REVERT: C 380 TYR cc_start: 0.8138 (m-10) cc_final: 0.7752 (m-10) REVERT: C 417 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8977 (tttt) REVERT: C 424 LYS cc_start: 0.8469 (tptt) cc_final: 0.7431 (mttt) REVERT: C 869 MET cc_start: 0.9029 (mtt) cc_final: 0.8412 (mtt) REVERT: C 960 ASN cc_start: 0.9091 (m-40) cc_final: 0.8849 (t0) REVERT: H 91 TYR cc_start: 0.5920 (OUTLIER) cc_final: 0.4901 (m-80) REVERT: L 4 MET cc_start: 0.6134 (mtm) cc_final: 0.5850 (mtm) REVERT: L 123 GLU cc_start: 0.7669 (pt0) cc_final: 0.7121 (pm20) REVERT: M 82 MET cc_start: 0.8480 (mtm) cc_final: 0.7880 (mmm) REVERT: M 218 LYS cc_start: 0.8351 (mttt) cc_final: 0.7964 (tptt) REVERT: M 228 LYS cc_start: 0.5882 (ttmt) cc_final: 0.5402 (pttm) outliers start: 61 outliers final: 47 residues processed: 233 average time/residue: 0.3696 time to fit residues: 130.0153 Evaluate side-chains 228 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 73 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 373 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 134 optimal weight: 0.0270 chunk 84 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 925 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 207 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079205 restraints weight = 176819.467| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.55 r_work: 0.3303 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 31034 Z= 0.117 Angle : 0.523 16.149 42351 Z= 0.267 Chirality : 0.043 0.481 5014 Planarity : 0.003 0.047 5314 Dihedral : 5.518 59.789 5456 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.31 % Allowed : 9.79 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3692 helix: 1.42 (0.20), residues: 738 sheet: -0.16 (0.16), residues: 1034 loop : -0.31 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.023 0.001 TYR B 380 PHE 0.015 0.001 PHE C 392 TRP 0.006 0.001 TRP B 104 HIS 0.002 0.000 HIS K 87 Details of bonding type rmsd covalent geometry : bond 0.00259 (30921) covalent geometry : angle 0.49407 (42056) SS BOND : bond 0.00326 ( 44) SS BOND : angle 2.18570 ( 88) hydrogen bonds : bond 0.03552 ( 1266) hydrogen bonds : angle 5.57615 ( 3651) link_ALPHA1-2 : bond 0.00134 ( 1) link_ALPHA1-2 : angle 1.87175 ( 3) link_ALPHA1-3 : bond 0.00910 ( 2) link_ALPHA1-3 : angle 2.35902 ( 6) link_ALPHA1-6 : bond 0.00332 ( 3) link_ALPHA1-6 : angle 1.60418 ( 9) link_BETA1-3 : bond 0.00389 ( 2) link_BETA1-3 : angle 2.42444 ( 6) link_BETA1-4 : bond 0.00279 ( 16) link_BETA1-4 : angle 1.31186 ( 48) link_BETA1-6 : bond 0.00368 ( 1) link_BETA1-6 : angle 1.73999 ( 3) link_NAG-ASN : bond 0.00341 ( 44) link_NAG-ASN : angle 2.30816 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7016 (mmt180) REVERT: A 195 LYS cc_start: 0.8749 (pttt) cc_final: 0.8331 (pttt) REVERT: A 204 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.6966 (m-80) REVERT: A 571 ASP cc_start: 0.7839 (t0) cc_final: 0.7317 (t0) REVERT: B 41 LYS cc_start: 0.7853 (mttp) cc_final: 0.7608 (mtmt) REVERT: B 52 GLN cc_start: 0.8853 (tt0) cc_final: 0.8152 (tm-30) REVERT: B 204 TYR cc_start: 0.7737 (m-80) cc_final: 0.7221 (m-80) REVERT: B 270 LEU cc_start: 0.8107 (mt) cc_final: 0.7837 (mt) REVERT: B 369 TYR cc_start: 0.8890 (t80) cc_final: 0.8669 (t80) REVERT: B 370 ASN cc_start: 0.8760 (m-40) cc_final: 0.8522 (p0) REVERT: B 740 MET cc_start: 0.8853 (ttt) cc_final: 0.8604 (mtp) REVERT: C 52 GLN cc_start: 0.8353 (tt0) cc_final: 0.7957 (pp30) REVERT: C 135 PHE cc_start: 0.8351 (m-80) cc_final: 0.8031 (m-10) REVERT: C 351 TYR cc_start: 0.8037 (p90) cc_final: 0.7696 (p90) REVERT: C 380 TYR cc_start: 0.8059 (m-80) cc_final: 0.7669 (m-10) REVERT: C 417 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8964 (tttt) REVERT: C 424 LYS cc_start: 0.8591 (tptt) cc_final: 0.7567 (mttt) REVERT: C 759 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.7883 (t80) REVERT: C 869 MET cc_start: 0.8934 (mtt) cc_final: 0.8402 (mtt) REVERT: C 960 ASN cc_start: 0.9013 (m-40) cc_final: 0.8766 (t0) REVERT: L 4 MET cc_start: 0.6057 (mtm) cc_final: 0.5796 (mtm) REVERT: L 123 GLU cc_start: 0.7714 (pt0) cc_final: 0.7171 (pm20) REVERT: M 82 MET cc_start: 0.8470 (mtm) cc_final: 0.8109 (mtt) REVERT: M 218 LYS cc_start: 0.8310 (mttt) cc_final: 0.7900 (tptt) outliers start: 43 outliers final: 33 residues processed: 218 average time/residue: 0.3689 time to fit residues: 121.6465 Evaluate side-chains 213 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 126 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 318 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 chunk 184 optimal weight: 0.0570 chunk 221 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.077560 restraints weight = 177223.737| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.80 r_work: 0.3272 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31034 Z= 0.185 Angle : 0.547 15.723 42351 Z= 0.278 Chirality : 0.043 0.479 5014 Planarity : 0.003 0.047 5314 Dihedral : 5.429 57.651 5456 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.52 % Allowed : 9.73 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3692 helix: 1.32 (0.20), residues: 745 sheet: -0.18 (0.16), residues: 1031 loop : -0.41 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 214 TYR 0.016 0.001 TYR M 185 PHE 0.015 0.001 PHE C1089 TRP 0.007 0.001 TRP H 157 HIS 0.027 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00415 (30921) covalent geometry : angle 0.52019 (42056) SS BOND : bond 0.00341 ( 44) SS BOND : angle 2.02565 ( 88) hydrogen bonds : bond 0.03607 ( 1266) hydrogen bonds : angle 5.56379 ( 3651) link_ALPHA1-2 : bond 0.00390 ( 1) link_ALPHA1-2 : angle 2.19946 ( 3) link_ALPHA1-3 : bond 0.00928 ( 2) link_ALPHA1-3 : angle 2.45854 ( 6) link_ALPHA1-6 : bond 0.00280 ( 3) link_ALPHA1-6 : angle 1.95839 ( 9) link_BETA1-3 : bond 0.00335 ( 2) link_BETA1-3 : angle 2.34371 ( 6) link_BETA1-4 : bond 0.00245 ( 16) link_BETA1-4 : angle 1.32806 ( 48) link_BETA1-6 : bond 0.00426 ( 1) link_BETA1-6 : angle 1.55019 ( 3) link_NAG-ASN : bond 0.00357 ( 44) link_NAG-ASN : angle 2.33099 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7018 (mmt180) REVERT: A 195 LYS cc_start: 0.8732 (pttt) cc_final: 0.8345 (pttt) REVERT: A 204 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: A 571 ASP cc_start: 0.7835 (t0) cc_final: 0.7343 (t0) REVERT: B 52 GLN cc_start: 0.8987 (tt0) cc_final: 0.8395 (tm-30) REVERT: B 204 TYR cc_start: 0.7823 (m-80) cc_final: 0.7366 (m-80) REVERT: B 270 LEU cc_start: 0.8276 (mt) cc_final: 0.7983 (mt) REVERT: B 740 MET cc_start: 0.8896 (ttt) cc_final: 0.8644 (mtp) REVERT: C 52 GLN cc_start: 0.8420 (tt0) cc_final: 0.8052 (pp30) REVERT: C 135 PHE cc_start: 0.8399 (m-80) cc_final: 0.8046 (m-10) REVERT: C 380 TYR cc_start: 0.8052 (m-80) cc_final: 0.7645 (m-10) REVERT: C 417 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8976 (tttt) REVERT: C 424 LYS cc_start: 0.8727 (tptt) cc_final: 0.7814 (mttt) REVERT: C 759 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 869 MET cc_start: 0.8972 (mtt) cc_final: 0.8402 (mtt) REVERT: C 960 ASN cc_start: 0.9061 (m-40) cc_final: 0.8823 (t0) REVERT: L 4 MET cc_start: 0.6166 (mtm) cc_final: 0.5909 (mtm) REVERT: L 123 GLU cc_start: 0.7659 (pt0) cc_final: 0.7121 (pm20) REVERT: M 82 MET cc_start: 0.8484 (mtm) cc_final: 0.8083 (mtm) REVERT: M 218 LYS cc_start: 0.8336 (mttt) cc_final: 0.7937 (tptt) REVERT: M 228 LYS cc_start: 0.5928 (ttmt) cc_final: 0.5482 (pttm) outliers start: 50 outliers final: 41 residues processed: 227 average time/residue: 0.3604 time to fit residues: 121.4795 Evaluate side-chains 223 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 302 optimal weight: 9.9990 chunk 285 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 chunk 341 optimal weight: 30.0000 chunk 245 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1113 GLN B 207 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 388 ASN C 501 ASN C 655 HIS C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073134 restraints weight = 170516.517| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.89 r_work: 0.3241 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 31034 Z= 0.348 Angle : 0.727 16.137 42351 Z= 0.366 Chirality : 0.047 0.468 5014 Planarity : 0.005 0.061 5314 Dihedral : 6.179 55.598 5452 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.82 % Allowed : 9.73 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 3692 helix: 0.54 (0.19), residues: 743 sheet: -0.53 (0.15), residues: 1042 loop : -0.74 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 214 TYR 0.042 0.002 TYR K 173 PHE 0.036 0.002 PHE B 906 TRP 0.014 0.002 TRP C 104 HIS 0.014 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00783 (30921) covalent geometry : angle 0.70067 (42056) SS BOND : bond 0.00433 ( 44) SS BOND : angle 2.25823 ( 88) hydrogen bonds : bond 0.04237 ( 1266) hydrogen bonds : angle 6.03307 ( 3651) link_ALPHA1-2 : bond 0.00767 ( 1) link_ALPHA1-2 : angle 2.89725 ( 3) link_ALPHA1-3 : bond 0.00699 ( 2) link_ALPHA1-3 : angle 3.07496 ( 6) link_ALPHA1-6 : bond 0.00655 ( 3) link_ALPHA1-6 : angle 2.97037 ( 9) link_BETA1-3 : bond 0.00207 ( 2) link_BETA1-3 : angle 2.78543 ( 6) link_BETA1-4 : bond 0.00419 ( 16) link_BETA1-4 : angle 1.53175 ( 48) link_BETA1-6 : bond 0.00372 ( 1) link_BETA1-6 : angle 1.51910 ( 3) link_NAG-ASN : bond 0.00587 ( 44) link_NAG-ASN : angle 2.67032 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7604 (p0) cc_final: 0.7138 (p0) REVERT: A 190 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7037 (mmt90) REVERT: A 378 LYS cc_start: 0.7972 (tptp) cc_final: 0.7771 (tptp) REVERT: A 505 TYR cc_start: 0.8369 (m-80) cc_final: 0.7973 (t80) REVERT: A 571 ASP cc_start: 0.7923 (t0) cc_final: 0.7535 (t0) REVERT: B 52 GLN cc_start: 0.9045 (tt0) cc_final: 0.8503 (tm-30) REVERT: B 204 TYR cc_start: 0.7863 (m-80) cc_final: 0.7209 (m-80) REVERT: C 52 GLN cc_start: 0.8514 (tt0) cc_final: 0.8298 (pp30) REVERT: C 135 PHE cc_start: 0.8438 (m-80) cc_final: 0.8175 (m-10) REVERT: C 417 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.8949 (tttt) REVERT: C 424 LYS cc_start: 0.8862 (tptt) cc_final: 0.7933 (mttt) REVERT: C 869 MET cc_start: 0.9020 (mtt) cc_final: 0.8431 (mtt) REVERT: C 960 ASN cc_start: 0.9033 (m-40) cc_final: 0.8798 (t0) REVERT: L 4 MET cc_start: 0.6539 (mtm) cc_final: 0.6187 (mtm) REVERT: L 123 GLU cc_start: 0.7692 (pt0) cc_final: 0.7155 (pm20) REVERT: M 82 MET cc_start: 0.8623 (mtm) cc_final: 0.8235 (mtm) REVERT: M 218 LYS cc_start: 0.8470 (mttt) cc_final: 0.8044 (tptt) REVERT: M 228 LYS cc_start: 0.6150 (ttmt) cc_final: 0.5724 (pttm) outliers start: 60 outliers final: 48 residues processed: 229 average time/residue: 0.3310 time to fit residues: 115.1963 Evaluate side-chains 221 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 61 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 341 optimal weight: 30.0000 chunk 221 optimal weight: 0.4980 chunk 128 optimal weight: 20.0000 chunk 320 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 351 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.124376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075079 restraints weight = 175828.893| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 4.21 r_work: 0.3279 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31034 Z= 0.125 Angle : 0.530 14.926 42351 Z= 0.269 Chirality : 0.043 0.428 5014 Planarity : 0.004 0.044 5314 Dihedral : 5.505 54.416 5451 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.34 % Allowed : 10.24 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3692 helix: 1.20 (0.19), residues: 746 sheet: -0.40 (0.16), residues: 1042 loop : -0.49 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.039 0.001 TYR K 173 PHE 0.018 0.001 PHE K 80 TRP 0.012 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00280 (30921) covalent geometry : angle 0.50485 (42056) SS BOND : bond 0.00331 ( 44) SS BOND : angle 1.83275 ( 88) hydrogen bonds : bond 0.03503 ( 1266) hydrogen bonds : angle 5.55309 ( 3651) link_ALPHA1-2 : bond 0.00250 ( 1) link_ALPHA1-2 : angle 1.96579 ( 3) link_ALPHA1-3 : bond 0.00912 ( 2) link_ALPHA1-3 : angle 2.34966 ( 6) link_ALPHA1-6 : bond 0.00332 ( 3) link_ALPHA1-6 : angle 1.61238 ( 9) link_BETA1-3 : bond 0.00308 ( 2) link_BETA1-3 : angle 2.64086 ( 6) link_BETA1-4 : bond 0.00269 ( 16) link_BETA1-4 : angle 1.33227 ( 48) link_BETA1-6 : bond 0.00312 ( 1) link_BETA1-6 : angle 1.61432 ( 3) link_NAG-ASN : bond 0.00340 ( 44) link_NAG-ASN : angle 2.25050 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7726 (p0) cc_final: 0.7227 (p0) REVERT: A 190 ARG cc_start: 0.7660 (mtt180) cc_final: 0.6967 (mmt90) REVERT: A 378 LYS cc_start: 0.7839 (tptp) cc_final: 0.7519 (tptp) REVERT: A 505 TYR cc_start: 0.8463 (m-80) cc_final: 0.8048 (t80) REVERT: A 571 ASP cc_start: 0.7791 (t0) cc_final: 0.7293 (t0) REVERT: B 52 GLN cc_start: 0.9050 (tt0) cc_final: 0.8506 (tm-30) REVERT: B 204 TYR cc_start: 0.7719 (m-80) cc_final: 0.7453 (m-80) REVERT: B 229 LEU cc_start: 0.7838 (mp) cc_final: 0.7341 (tp) REVERT: B 270 LEU cc_start: 0.8337 (mt) cc_final: 0.8093 (mt) REVERT: B 571 ASP cc_start: 0.8645 (t0) cc_final: 0.8023 (t0) REVERT: B 740 MET cc_start: 0.8830 (ttt) cc_final: 0.8573 (mtp) REVERT: C 52 GLN cc_start: 0.8495 (tt0) cc_final: 0.8273 (pp30) REVERT: C 135 PHE cc_start: 0.8534 (m-80) cc_final: 0.8143 (m-10) REVERT: C 380 TYR cc_start: 0.8031 (m-80) cc_final: 0.7636 (m-10) REVERT: C 417 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9060 (tttt) REVERT: C 424 LYS cc_start: 0.8827 (tptt) cc_final: 0.8168 (ttpt) REVERT: C 869 MET cc_start: 0.8993 (mtt) cc_final: 0.8519 (mtt) REVERT: C 960 ASN cc_start: 0.8991 (m-40) cc_final: 0.8740 (t0) REVERT: L 4 MET cc_start: 0.6466 (mtm) cc_final: 0.6125 (mtm) REVERT: L 123 GLU cc_start: 0.7819 (pt0) cc_final: 0.7249 (pm20) REVERT: M 82 MET cc_start: 0.8527 (mtm) cc_final: 0.8125 (mtt) REVERT: M 117 LYS cc_start: 0.8959 (mttt) cc_final: 0.8665 (mppt) REVERT: M 218 LYS cc_start: 0.8480 (mttt) cc_final: 0.8089 (tptt) REVERT: M 228 LYS cc_start: 0.6190 (ttmt) cc_final: 0.5695 (pttt) outliers start: 44 outliers final: 40 residues processed: 215 average time/residue: 0.3862 time to fit residues: 123.0163 Evaluate side-chains 209 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain L residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 106 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.127488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.078016 restraints weight = 177400.262| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 4.79 r_work: 0.3277 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 31034 Z= 0.109 Angle : 0.507 14.319 42351 Z= 0.257 Chirality : 0.043 0.425 5014 Planarity : 0.003 0.046 5314 Dihedral : 5.157 53.713 5451 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.09 % Allowed : 10.49 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3692 helix: 1.48 (0.20), residues: 747 sheet: -0.15 (0.16), residues: 999 loop : -0.44 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 214 TYR 0.034 0.001 TYR K 173 PHE 0.015 0.001 PHE A 515 TRP 0.013 0.001 TRP A 104 HIS 0.018 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00243 (30921) covalent geometry : angle 0.48295 (42056) SS BOND : bond 0.00322 ( 44) SS BOND : angle 1.68918 ( 88) hydrogen bonds : bond 0.03354 ( 1266) hydrogen bonds : angle 5.37843 ( 3651) link_ALPHA1-2 : bond 0.00114 ( 1) link_ALPHA1-2 : angle 1.91624 ( 3) link_ALPHA1-3 : bond 0.00720 ( 2) link_ALPHA1-3 : angle 2.16308 ( 6) link_ALPHA1-6 : bond 0.00311 ( 3) link_ALPHA1-6 : angle 1.56920 ( 9) link_BETA1-3 : bond 0.00383 ( 2) link_BETA1-3 : angle 2.31244 ( 6) link_BETA1-4 : bond 0.00285 ( 16) link_BETA1-4 : angle 1.34472 ( 48) link_BETA1-6 : bond 0.00352 ( 1) link_BETA1-6 : angle 1.48482 ( 3) link_NAG-ASN : bond 0.00317 ( 44) link_NAG-ASN : angle 2.17969 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7384 Ramachandran restraints generated. 3692 Oldfield, 0 Emsley, 3692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7660 (p0) cc_final: 0.7153 (p0) REVERT: A 190 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6912 (mmt90) REVERT: A 571 ASP cc_start: 0.7767 (t0) cc_final: 0.7282 (t0) REVERT: B 52 GLN cc_start: 0.9056 (tt0) cc_final: 0.8526 (tm-30) REVERT: B 204 TYR cc_start: 0.7738 (m-80) cc_final: 0.7454 (m-80) REVERT: B 229 LEU cc_start: 0.7772 (mp) cc_final: 0.7297 (tp) REVERT: B 270 LEU cc_start: 0.8339 (mt) cc_final: 0.8058 (mt) REVERT: B 571 ASP cc_start: 0.8643 (t0) cc_final: 0.8094 (t0) REVERT: B 740 MET cc_start: 0.8716 (ttt) cc_final: 0.8505 (mtp) REVERT: C 135 PHE cc_start: 0.8554 (m-80) cc_final: 0.8157 (m-10) REVERT: C 417 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9079 (tttt) REVERT: C 424 LYS cc_start: 0.8833 (tptt) cc_final: 0.8207 (ttpt) REVERT: C 869 MET cc_start: 0.8912 (mtt) cc_final: 0.8471 (mtt) REVERT: C 960 ASN cc_start: 0.8971 (m-40) cc_final: 0.8727 (t0) REVERT: C 1005 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8853 (mm110) REVERT: H 82 MET cc_start: 0.7848 (mmm) cc_final: 0.7154 (mmm) REVERT: L 4 MET cc_start: 0.6391 (mtm) cc_final: 0.6053 (mtm) REVERT: L 123 GLU cc_start: 0.7874 (pt0) cc_final: 0.7368 (pm20) REVERT: M 26 ASN cc_start: 0.8369 (t0) cc_final: 0.7980 (t0) REVERT: M 82 MET cc_start: 0.8538 (mtm) cc_final: 0.8114 (mtt) REVERT: M 117 LYS cc_start: 0.8925 (mttt) cc_final: 0.8669 (mppt) REVERT: M 218 LYS cc_start: 0.8491 (mttt) cc_final: 0.8113 (tptt) REVERT: M 228 LYS cc_start: 0.5857 (ttmt) cc_final: 0.5606 (pttt) outliers start: 36 outliers final: 33 residues processed: 202 average time/residue: 0.2762 time to fit residues: 83.2485 Evaluate side-chains 205 residues out of total 3290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 126 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 267 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 362 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.123520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.072007 restraints weight = 176592.755| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.13 r_work: 0.3129 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31034 Z= 0.224 Angle : 0.574 14.184 42351 Z= 0.290 Chirality : 0.044 0.442 5014 Planarity : 0.004 0.044 5314 Dihedral : 5.355 54.493 5451 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.16 % Allowed : 10.61 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3692 helix: 1.26 (0.19), residues: 747 sheet: -0.28 (0.16), residues: 1028 loop : -0.55 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.031 0.002 TYR K 173 PHE 0.017 0.001 PHE C1089 TRP 0.010 0.001 TRP A 104 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00504 (30921) covalent geometry : angle 0.55022 (42056) SS BOND : bond 0.00349 ( 44) SS BOND : angle 1.78796 ( 88) hydrogen bonds : bond 0.03600 ( 1266) hydrogen bonds : angle 5.54925 ( 3651) link_ALPHA1-2 : bond 0.00525 ( 1) link_ALPHA1-2 : angle 2.44724 ( 3) link_ALPHA1-3 : bond 0.00793 ( 2) link_ALPHA1-3 : angle 2.56748 ( 6) link_ALPHA1-6 : bond 0.00285 ( 3) link_ALPHA1-6 : angle 2.16988 ( 9) link_BETA1-3 : bond 0.00245 ( 2) link_BETA1-3 : angle 2.47935 ( 6) link_BETA1-4 : bond 0.00315 ( 16) link_BETA1-4 : angle 1.39728 ( 48) link_BETA1-6 : bond 0.00449 ( 1) link_BETA1-6 : angle 1.45451 ( 3) link_NAG-ASN : bond 0.00389 ( 44) link_NAG-ASN : angle 2.30402 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12268.87 seconds wall clock time: 209 minutes 26.44 seconds (12566.44 seconds total)