Starting phenix.real_space_refine on Sun Jun 22 12:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.map" model { file = "/net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r18_14234/06_2025/7r18_14234.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16398 2.51 5 N 4218 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25773 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8315 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 54, 'TRANS': 1008} Chain breaks: 5 Chain: "B" Number of atoms: 8315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8315 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 54, 'TRANS': 1008} Chain breaks: 5 Chain: "C" Number of atoms: 8315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8315 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 54, 'TRANS': 1008} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 17.27, per 1000 atoms: 0.67 Number of scatterers: 25773 At special positions: 0 Unit cell: (157.388, 162.778, 178.948, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 5043 8.00 N 4218 7.00 C 16398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 17 " " NAG A1203 " - " ASN A 122 " " NAG A1204 " - " ASN A 165 " " NAG A1205 " - " ASN A 234 " " NAG A1206 " - " ASN A 343 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A 709 " " NAG A1210 " - " ASN A 801 " " NAG A1211 " - " ASN A1074 " " NAG A1212 " - " ASN A 282 " " NAG A1213 " - " ASN A 61 " " NAG B1201 " - " ASN B 331 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 122 " " NAG B1204 " - " ASN B 165 " " NAG B1205 " - " ASN B 234 " " NAG B1206 " - " ASN B 343 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 709 " " NAG B1210 " - " ASN B 801 " " NAG B1211 " - " ASN B1074 " " NAG B1212 " - " ASN B 282 " " NAG B1213 " - " ASN B 61 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 17 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 165 " " NAG C1205 " - " ASN C 234 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG C1210 " - " ASN C 801 " " NAG C1211 " - " ASN C1074 " " NAG C1212 " - " ASN C 282 " " NAG C1213 " - " ASN C 61 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C1134 " Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 7.3 seconds 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 23.7% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.787A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.130A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.893A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.985A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.591A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.776A 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: 4.074A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.017A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.885A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.504A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.612A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.170A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.786A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.129A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.893A pdb=" N GLN B 409 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.985A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.591A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.074A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.017A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.885A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.504A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.612A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.170A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.787A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.130A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.893A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.984A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 815 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.591A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.074A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.017A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.885A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.504A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.611A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.169A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.123A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 5.643A 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: 3.602A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.994A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 131 removed outlier: 3.519A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.665A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.345A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.597A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.184A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.850A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.596A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.596A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.687A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.571A pdb=" N ASN C 703 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.123A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.994A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 126 through 131 removed outlier: 3.519A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.666A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.345A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.596A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.184A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.866A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.123A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 126 through 131 removed outlier: 3.519A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.665A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.345A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.527A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.184A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 1020 hydrogen bonds defined for protein. 2853 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: 19.02 Time building geometry restraints manager: 9.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7551 1.33 - 1.46: 4864 1.46 - 1.58: 13796 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 26355 Sorted by residual: bond pdb=" N VAL B 524 " pdb=" CA VAL B 524 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.26e-02 6.30e+03 9.12e+00 bond pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.26e-02 6.30e+03 8.93e+00 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 bond pdb=" N VAL C 171 " pdb=" CA VAL C 171 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.87e+00 bond pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.18e-02 7.18e+03 8.86e+00 ... (remaining 26350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 33632 1.35 - 2.69: 1780 2.69 - 4.04: 382 4.04 - 5.39: 53 5.39 - 6.73: 18 Bond angle restraints: 35865 Sorted by residual: angle pdb=" CA THR A 124 " pdb=" C THR A 124 " pdb=" O THR A 124 " ideal model delta sigma weight residual 120.70 116.89 3.81 1.03e+00 9.43e-01 1.37e+01 angle pdb=" CA THR C 124 " pdb=" C THR C 124 " pdb=" O THR C 124 " ideal model delta sigma weight residual 120.70 116.91 3.79 1.03e+00 9.43e-01 1.35e+01 angle pdb=" CA THR B 124 " pdb=" C THR B 124 " pdb=" O THR B 124 " ideal model delta sigma weight residual 120.70 116.94 3.76 1.03e+00 9.43e-01 1.33e+01 angle pdb=" CA LEU C 582 " pdb=" C LEU C 582 " pdb=" O LEU C 582 " ideal model delta sigma weight residual 121.84 117.83 4.01 1.16e+00 7.43e-01 1.20e+01 angle pdb=" CA LEU A 582 " pdb=" C LEU A 582 " pdb=" O LEU A 582 " ideal model delta sigma weight residual 121.84 117.85 3.99 1.16e+00 7.43e-01 1.19e+01 ... (remaining 35860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 15434 17.62 - 35.24: 892 35.24 - 52.86: 116 52.86 - 70.48: 25 70.48 - 88.10: 6 Dihedral angle restraints: 16473 sinusoidal: 7200 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.10 88.10 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.08 88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -174.06 88.06 1 1.00e+01 1.00e-02 9.28e+01 ... (remaining 16470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3695 0.083 - 0.165: 488 0.165 - 0.248: 28 0.248 - 0.330: 10 0.330 - 0.413: 6 Chirality restraints: 4227 Sorted by residual: chirality pdb=" C1 NAG B1201 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1201 " pdb=" O5 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C1 NAG A1201 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1201 " pdb=" O5 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 ... (remaining 4224 not shown) Planarity restraints: 4623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1201 " 0.208 2.00e-02 2.50e+03 1.72e-01 3.70e+02 pdb=" C7 NAG B1201 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG B1201 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG B1201 " -0.280 2.00e-02 2.50e+03 pdb=" O7 NAG B1201 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1201 " 0.208 2.00e-02 2.50e+03 1.72e-01 3.70e+02 pdb=" C7 NAG C1201 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1201 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG C1201 " -0.280 2.00e-02 2.50e+03 pdb=" O7 NAG C1201 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1201 " -0.208 2.00e-02 2.50e+03 1.72e-01 3.70e+02 pdb=" C7 NAG A1201 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG A1201 " -0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A1201 " 0.280 2.00e-02 2.50e+03 pdb=" O7 NAG A1201 " 0.020 2.00e-02 2.50e+03 ... (remaining 4620 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2948 2.75 - 3.29: 23469 3.29 - 3.82: 39523 3.82 - 4.36: 48320 4.36 - 4.90: 84313 Nonbonded interactions: 198573 Sorted by model distance: nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.212 3.040 nonbonded pdb=" NE2 GLN A 965 " pdb=" O GLY B 757 " model vdw 2.278 3.120 nonbonded pdb=" NE2 GLN B 965 " pdb=" O GLY C 757 " model vdw 2.295 3.120 ... (remaining 198568 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 30.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 77.760 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 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:92.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 0.006 0.058 26457 Z= 0.298 Angle : 0.726 6.894 36129 Z= 0.422 Chirality : 0.055 0.413 4227 Planarity : 0.006 0.172 4575 Dihedral : 10.844 74.888 10383 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.32 % Allowed : 0.43 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3153 helix: 2.24 (0.20), residues: 612 sheet: 0.70 (0.19), residues: 702 loop : -0.77 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 886 HIS 0.007 0.001 HIS C1064 PHE 0.042 0.002 PHE B 906 TYR 0.018 0.002 TYR B 265 ARG 0.004 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 1.82637 ( 144) link_BETA1-4 : bond 0.00352 ( 9) link_BETA1-4 : angle 1.15652 ( 27) hydrogen bonds : bond 0.13816 ( 969) hydrogen bonds : angle 6.58655 ( 2853) link_BETA1-6 : bond 0.00129 ( 3) link_BETA1-6 : angle 1.54259 ( 9) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.77077 ( 84) covalent geometry : bond 0.00573 (26355) covalent geometry : angle 0.71318 (35865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 319 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 ASN cc_start: 0.5980 (t160) cc_final: 0.5643 (t0) REVERT: B 794 ILE cc_start: 0.8246 (mm) cc_final: 0.7788 (pp) REVERT: C 794 ILE cc_start: 0.8233 (mm) cc_final: 0.7508 (pp) outliers start: 9 outliers final: 4 residues processed: 320 average time/residue: 1.2042 time to fit residues: 466.9233 Evaluate side-chains 180 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 176 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain C residue 188 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 151 optimal weight: 0.0060 chunk 185 optimal weight: 1.9990 chunk 288 optimal weight: 0.9980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN A 580 GLN A 755 GLN A 804 GLN A 957 GLN A1002 GLN A1010 GLN B 188 ASN B 394 ASN B 532 ASN B 580 GLN B 804 GLN B 957 GLN B1002 GLN B1010 GLN C 188 ASN C 207 HIS C 532 ASN C 580 GLN C 804 GLN C 957 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.184004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138212 restraints weight = 32721.261| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.23 r_work: 0.3180 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26457 Z= 0.131 Angle : 0.562 10.082 36129 Z= 0.290 Chirality : 0.044 0.188 4227 Planarity : 0.004 0.036 4575 Dihedral : 5.691 54.386 4674 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.54 % Allowed : 5.78 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3153 helix: 2.67 (0.21), residues: 612 sheet: 0.60 (0.19), residues: 684 loop : -0.72 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.021 0.001 PHE C 906 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG A1014 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 48) link_NAG-ASN : angle 1.69957 ( 144) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.06430 ( 27) hydrogen bonds : bond 0.06339 ( 969) hydrogen bonds : angle 5.37900 ( 2853) link_BETA1-6 : bond 0.00349 ( 3) link_BETA1-6 : angle 1.32630 ( 9) SS BOND : bond 0.00185 ( 42) SS BOND : angle 1.08638 ( 84) covalent geometry : bond 0.00292 (26355) covalent geometry : angle 0.54983 (35865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7176 (mttm) REVERT: A 378 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7635 (ttpp) REVERT: A 1119 ASN cc_start: 0.7916 (m-40) cc_final: 0.7710 (m110) REVERT: B 794 ILE cc_start: 0.8341 (mm) cc_final: 0.7635 (pp) REVERT: C 794 ILE cc_start: 0.8274 (mm) cc_final: 0.7481 (pp) outliers start: 43 outliers final: 16 residues processed: 210 average time/residue: 1.1201 time to fit residues: 291.3754 Evaluate side-chains 172 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 4.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 758 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 HIS A 957 GLN B 188 ASN B 196 ASN B 394 ASN B 957 GLN B1010 GLN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.181604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.135215 restraints weight = 32665.392| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.30 r_work: 0.3126 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26457 Z= 0.188 Angle : 0.593 9.610 36129 Z= 0.304 Chirality : 0.046 0.171 4227 Planarity : 0.004 0.035 4575 Dihedral : 5.463 54.827 4667 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 7.39 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3153 helix: 2.50 (0.21), residues: 630 sheet: 0.38 (0.19), residues: 678 loop : -0.83 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 886 HIS 0.007 0.001 HIS A1058 PHE 0.025 0.002 PHE C 906 TYR 0.020 0.002 TYR C1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 48) link_NAG-ASN : angle 1.65496 ( 144) link_BETA1-4 : bond 0.00210 ( 9) link_BETA1-4 : angle 1.19265 ( 27) hydrogen bonds : bond 0.07206 ( 969) hydrogen bonds : angle 5.31511 ( 2853) link_BETA1-6 : bond 0.00181 ( 3) link_BETA1-6 : angle 1.30908 ( 9) SS BOND : bond 0.00226 ( 42) SS BOND : angle 1.23881 ( 84) covalent geometry : bond 0.00465 (26355) covalent geometry : angle 0.58122 (35865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 2.816 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6774 (t80) REVERT: B 196 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (m-40) REVERT: B 794 ILE cc_start: 0.8404 (mm) cc_final: 0.7689 (pp) REVERT: C 423 TYR cc_start: 0.8545 (t80) cc_final: 0.7986 (t80) REVERT: C 794 ILE cc_start: 0.8378 (mm) cc_final: 0.7545 (pp) outliers start: 49 outliers final: 24 residues processed: 199 average time/residue: 0.9383 time to fit residues: 234.2484 Evaluate side-chains 184 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 1.9990 chunk 279 optimal weight: 0.4980 chunk 306 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 286 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 285 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 957 GLN B 188 ASN B 196 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1010 GLN C 188 ASN C 394 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137502 restraints weight = 32826.366| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.32 r_work: 0.3165 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26457 Z= 0.118 Angle : 0.537 11.841 36129 Z= 0.273 Chirality : 0.044 0.179 4227 Planarity : 0.004 0.036 4575 Dihedral : 5.210 54.896 4667 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.47 % Allowed : 8.90 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3153 helix: 2.79 (0.21), residues: 612 sheet: 0.66 (0.19), residues: 660 loop : -0.88 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 PHE 0.013 0.001 PHE C 32 TYR 0.019 0.001 TYR A 396 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 1.57502 ( 144) link_BETA1-4 : bond 0.00323 ( 9) link_BETA1-4 : angle 1.08984 ( 27) hydrogen bonds : bond 0.05897 ( 969) hydrogen bonds : angle 5.01955 ( 2853) link_BETA1-6 : bond 0.00291 ( 3) link_BETA1-6 : angle 1.22004 ( 9) SS BOND : bond 0.00171 ( 42) SS BOND : angle 0.87180 ( 84) covalent geometry : bond 0.00262 (26355) covalent geometry : angle 0.52645 (35865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 2.867 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6767 (t80) REVERT: A 378 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7676 (ttpp) REVERT: A 394 ASN cc_start: 0.7243 (p0) cc_final: 0.7017 (p0) REVERT: A 1119 ASN cc_start: 0.7930 (m-40) cc_final: 0.7711 (m110) REVERT: B 564 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: B 794 ILE cc_start: 0.8359 (mm) cc_final: 0.7657 (pp) REVERT: C 392 PHE cc_start: 0.7575 (m-80) cc_final: 0.7268 (m-80) REVERT: C 423 TYR cc_start: 0.8512 (t80) cc_final: 0.7998 (t80) REVERT: C 564 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: C 794 ILE cc_start: 0.8313 (mm) cc_final: 0.7500 (pp) REVERT: C 1119 ASN cc_start: 0.8017 (m-40) cc_final: 0.7765 (m110) outliers start: 41 outliers final: 18 residues processed: 201 average time/residue: 0.9864 time to fit residues: 245.4051 Evaluate side-chains 176 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 164 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 422 ASN A 957 GLN B 188 ASN B 394 ASN B 422 ASN B1010 GLN C 30 ASN C 188 ASN C 422 ASN C 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.180007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135225 restraints weight = 32772.569| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.44 r_work: 0.3107 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 26457 Z= 0.243 Angle : 0.637 11.084 36129 Z= 0.325 Chirality : 0.048 0.172 4227 Planarity : 0.004 0.040 4575 Dihedral : 5.406 55.631 4667 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.94 % Allowed : 9.83 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3153 helix: 2.37 (0.21), residues: 630 sheet: 0.44 (0.19), residues: 648 loop : -0.98 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 886 HIS 0.008 0.001 HIS A1064 PHE 0.024 0.002 PHE A1121 TYR 0.020 0.002 TYR A 396 ARG 0.006 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 48) link_NAG-ASN : angle 1.68978 ( 144) link_BETA1-4 : bond 0.00172 ( 9) link_BETA1-4 : angle 1.23070 ( 27) hydrogen bonds : bond 0.07771 ( 969) hydrogen bonds : angle 5.25080 ( 2853) link_BETA1-6 : bond 0.00087 ( 3) link_BETA1-6 : angle 1.33852 ( 9) SS BOND : bond 0.00292 ( 42) SS BOND : angle 1.61507 ( 84) covalent geometry : bond 0.00614 (26355) covalent geometry : angle 0.62410 (35865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 2.962 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7679 (ttpp) REVERT: A 394 ASN cc_start: 0.7250 (p0) cc_final: 0.6943 (p0) REVERT: A 396 TYR cc_start: 0.8785 (m-80) cc_final: 0.8580 (m-80) REVERT: B 177 MET cc_start: 0.5274 (pmm) cc_final: 0.5061 (pmt) REVERT: B 529 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7714 (mmpt) REVERT: B 794 ILE cc_start: 0.8481 (mm) cc_final: 0.7895 (pp) REVERT: C 392 PHE cc_start: 0.7747 (m-80) cc_final: 0.7444 (m-80) REVERT: C 423 TYR cc_start: 0.8632 (t80) cc_final: 0.8162 (t80) REVERT: C 794 ILE cc_start: 0.8378 (mm) cc_final: 0.7616 (pp) outliers start: 54 outliers final: 31 residues processed: 200 average time/residue: 1.0141 time to fit residues: 252.6743 Evaluate side-chains 193 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 279 optimal weight: 0.9990 chunk 240 optimal weight: 0.6980 chunk 219 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 264 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 957 GLN A1002 GLN B 188 ASN B 957 GLN B1010 GLN C 30 ASN C 188 ASN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137020 restraints weight = 32693.935| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.42 r_work: 0.3125 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26457 Z= 0.166 Angle : 0.583 11.683 36129 Z= 0.296 Chirality : 0.045 0.173 4227 Planarity : 0.004 0.041 4575 Dihedral : 5.315 54.971 4667 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.90 % Allowed : 10.44 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3153 helix: 2.45 (0.21), residues: 630 sheet: 0.49 (0.19), residues: 648 loop : -1.00 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.006 0.001 HIS A1064 PHE 0.020 0.001 PHE B 32 TYR 0.019 0.001 TYR B 396 ARG 0.003 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 48) link_NAG-ASN : angle 1.62177 ( 144) link_BETA1-4 : bond 0.00242 ( 9) link_BETA1-4 : angle 1.10520 ( 27) hydrogen bonds : bond 0.06803 ( 969) hydrogen bonds : angle 5.07900 ( 2853) link_BETA1-6 : bond 0.00183 ( 3) link_BETA1-6 : angle 1.28867 ( 9) SS BOND : bond 0.00231 ( 42) SS BOND : angle 1.50276 ( 84) covalent geometry : bond 0.00402 (26355) covalent geometry : angle 0.57006 (35865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: A 394 ASN cc_start: 0.7250 (p0) cc_final: 0.6964 (p0) REVERT: B 529 LYS cc_start: 0.7956 (mmpt) cc_final: 0.7687 (mmpt) REVERT: B 794 ILE cc_start: 0.8416 (mm) cc_final: 0.7683 (pp) REVERT: C 140 PHE cc_start: 0.7669 (p90) cc_final: 0.7429 (p90) REVERT: C 392 PHE cc_start: 0.7735 (m-80) cc_final: 0.7454 (m-80) REVERT: C 423 TYR cc_start: 0.8666 (t80) cc_final: 0.8163 (t80) REVERT: C 564 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: C 794 ILE cc_start: 0.8376 (mm) cc_final: 0.7622 (pp) outliers start: 53 outliers final: 32 residues processed: 204 average time/residue: 0.9398 time to fit residues: 242.0914 Evaluate side-chains 190 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 298 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B 957 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.182089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136038 restraints weight = 32798.641| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.31 r_work: 0.3141 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26457 Z= 0.144 Angle : 0.575 12.254 36129 Z= 0.288 Chirality : 0.045 0.183 4227 Planarity : 0.004 0.039 4575 Dihedral : 5.234 54.721 4667 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.54 % Allowed : 11.30 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3153 helix: 2.56 (0.21), residues: 630 sheet: 0.54 (0.19), residues: 639 loop : -1.02 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.004 0.001 HIS A1064 PHE 0.021 0.001 PHE A 32 TYR 0.020 0.001 TYR B 396 ARG 0.003 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 48) link_NAG-ASN : angle 1.58587 ( 144) link_BETA1-4 : bond 0.00304 ( 9) link_BETA1-4 : angle 1.07226 ( 27) hydrogen bonds : bond 0.06326 ( 969) hydrogen bonds : angle 4.96408 ( 2853) link_BETA1-6 : bond 0.00241 ( 3) link_BETA1-6 : angle 1.25380 ( 9) SS BOND : bond 0.00202 ( 42) SS BOND : angle 1.44503 ( 84) covalent geometry : bond 0.00342 (26355) covalent geometry : angle 0.56241 (35865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6927 (mt0) REVERT: A 378 LYS cc_start: 0.7983 (tttm) cc_final: 0.7729 (tttp) REVERT: B 177 MET cc_start: 0.4895 (pmt) cc_final: 0.4689 (pmm) REVERT: B 529 LYS cc_start: 0.8031 (mmpt) cc_final: 0.7722 (mmpt) REVERT: B 794 ILE cc_start: 0.8403 (mm) cc_final: 0.7691 (pp) REVERT: C 140 PHE cc_start: 0.7751 (p90) cc_final: 0.7440 (p90) REVERT: C 392 PHE cc_start: 0.7681 (m-80) cc_final: 0.7387 (m-80) REVERT: C 423 TYR cc_start: 0.8655 (t80) cc_final: 0.8116 (t80) REVERT: C 564 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7868 (mm-40) REVERT: C 794 ILE cc_start: 0.8358 (mm) cc_final: 0.7792 (pp) outliers start: 43 outliers final: 27 residues processed: 193 average time/residue: 0.8607 time to fit residues: 207.9470 Evaluate side-chains 186 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 36 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 218 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 317 optimal weight: 0.9990 chunk 217 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN C 188 ASN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.182360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.136012 restraints weight = 32652.541| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.20 r_work: 0.3117 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26457 Z= 0.136 Angle : 0.568 11.864 36129 Z= 0.286 Chirality : 0.044 0.193 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.149 54.629 4665 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.47 % Allowed : 11.34 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3153 helix: 2.71 (0.21), residues: 612 sheet: 0.59 (0.20), residues: 639 loop : -1.04 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS A1064 PHE 0.013 0.001 PHE A1121 TYR 0.022 0.001 TYR B 396 ARG 0.003 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 48) link_NAG-ASN : angle 1.56000 ( 144) link_BETA1-4 : bond 0.00285 ( 9) link_BETA1-4 : angle 1.05135 ( 27) hydrogen bonds : bond 0.06085 ( 969) hydrogen bonds : angle 4.88519 ( 2853) link_BETA1-6 : bond 0.00249 ( 3) link_BETA1-6 : angle 1.24669 ( 9) SS BOND : bond 0.00184 ( 42) SS BOND : angle 1.21563 ( 84) covalent geometry : bond 0.00321 (26355) covalent geometry : angle 0.55726 (35865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 2.903 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6917 (mt0) REVERT: A 353 TRP cc_start: 0.8136 (p-90) cc_final: 0.7746 (p-90) REVERT: A 378 LYS cc_start: 0.7960 (tttm) cc_final: 0.7756 (ttpp) REVERT: A 396 TYR cc_start: 0.8748 (m-80) cc_final: 0.8524 (m-80) REVERT: A 1119 ASN cc_start: 0.8000 (m-40) cc_final: 0.7768 (m110) REVERT: B 423 TYR cc_start: 0.8548 (t80) cc_final: 0.8321 (t80) REVERT: B 529 LYS cc_start: 0.8076 (mmpt) cc_final: 0.7747 (mmpt) REVERT: B 794 ILE cc_start: 0.8371 (mm) cc_final: 0.7662 (pp) REVERT: C 140 PHE cc_start: 0.7877 (p90) cc_final: 0.7544 (p90) REVERT: C 392 PHE cc_start: 0.7682 (m-80) cc_final: 0.7377 (m-80) REVERT: C 423 TYR cc_start: 0.8663 (t80) cc_final: 0.8073 (t80) REVERT: C 564 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7917 (mm-40) REVERT: C 794 ILE cc_start: 0.8351 (mm) cc_final: 0.7765 (pp) REVERT: C 1119 ASN cc_start: 0.8079 (m-40) cc_final: 0.7815 (m110) outliers start: 41 outliers final: 32 residues processed: 191 average time/residue: 0.8700 time to fit residues: 211.1815 Evaluate side-chains 193 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 60 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 258 optimal weight: 50.0000 chunk 239 optimal weight: 0.2980 chunk 88 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.179069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131743 restraints weight = 32685.973| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.55 r_work: 0.3053 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 26457 Z= 0.262 Angle : 0.672 12.102 36129 Z= 0.340 Chirality : 0.049 0.182 4227 Planarity : 0.004 0.049 4575 Dihedral : 5.453 55.526 4665 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.44 % Allowed : 11.88 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3153 helix: 2.27 (0.21), residues: 630 sheet: 0.45 (0.19), residues: 672 loop : -1.16 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.009 0.001 HIS A1064 PHE 0.026 0.002 PHE A1121 TYR 0.021 0.002 TYR B 396 ARG 0.006 0.001 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 48) link_NAG-ASN : angle 1.73844 ( 144) link_BETA1-4 : bond 0.00192 ( 9) link_BETA1-4 : angle 1.23273 ( 27) hydrogen bonds : bond 0.08096 ( 969) hydrogen bonds : angle 5.21078 ( 2853) link_BETA1-6 : bond 0.00076 ( 3) link_BETA1-6 : angle 1.33077 ( 9) SS BOND : bond 0.00331 ( 42) SS BOND : angle 1.92632 ( 84) covalent geometry : bond 0.00658 (26355) covalent geometry : angle 0.65787 (35865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 2.915 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6646 (mt0) REVERT: A 353 TRP cc_start: 0.8288 (p-90) cc_final: 0.7929 (p-90) REVERT: B 378 LYS cc_start: 0.7938 (ptmm) cc_final: 0.7568 (tttp) REVERT: B 794 ILE cc_start: 0.8404 (mm) cc_final: 0.7680 (pp) REVERT: C 140 PHE cc_start: 0.7914 (p90) cc_final: 0.7523 (p90) REVERT: C 392 PHE cc_start: 0.7823 (m-80) cc_final: 0.7537 (m-80) REVERT: C 423 TYR cc_start: 0.8758 (t80) cc_final: 0.8131 (t80) REVERT: C 564 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7854 (mm-40) REVERT: C 794 ILE cc_start: 0.8412 (mm) cc_final: 0.7789 (pp) outliers start: 40 outliers final: 32 residues processed: 188 average time/residue: 0.9148 time to fit residues: 215.3408 Evaluate side-chains 189 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 252 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 210 optimal weight: 0.0980 chunk 214 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 188 ASN B 957 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134830 restraints weight = 32568.729| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.46 r_work: 0.3102 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26457 Z= 0.156 Angle : 0.607 12.202 36129 Z= 0.303 Chirality : 0.045 0.192 4227 Planarity : 0.004 0.045 4575 Dihedral : 5.401 54.718 4665 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 12.09 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3153 helix: 2.44 (0.21), residues: 630 sheet: 0.36 (0.20), residues: 627 loop : -1.08 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.005 0.001 HIS A1064 PHE 0.023 0.001 PHE B 32 TYR 0.023 0.001 TYR B 396 ARG 0.003 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 48) link_NAG-ASN : angle 1.70530 ( 144) link_BETA1-4 : bond 0.00270 ( 9) link_BETA1-4 : angle 1.07041 ( 27) hydrogen bonds : bond 0.06609 ( 969) hydrogen bonds : angle 4.97329 ( 2853) link_BETA1-6 : bond 0.00204 ( 3) link_BETA1-6 : angle 1.28356 ( 9) SS BOND : bond 0.00204 ( 42) SS BOND : angle 1.44255 ( 84) covalent geometry : bond 0.00374 (26355) covalent geometry : angle 0.59460 (35865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6306 Ramachandran restraints generated. 3153 Oldfield, 0 Emsley, 3153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6990 (mt0) REVERT: B 564 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8116 (mm-40) REVERT: B 794 ILE cc_start: 0.8469 (mm) cc_final: 0.7727 (pp) REVERT: C 140 PHE cc_start: 0.7883 (p90) cc_final: 0.7490 (p90) REVERT: C 392 PHE cc_start: 0.7773 (m-80) cc_final: 0.7487 (m-80) REVERT: C 423 TYR cc_start: 0.8746 (t80) cc_final: 0.8140 (t80) REVERT: C 564 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7904 (mm-40) REVERT: C 794 ILE cc_start: 0.8406 (mm) cc_final: 0.7815 (pp) outliers start: 40 outliers final: 33 residues processed: 184 average time/residue: 0.9017 time to fit residues: 210.7646 Evaluate side-chains 188 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 310 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B 957 GLN B1010 GLN C 188 ASN C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.181746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134281 restraints weight = 32645.495| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.52 r_work: 0.3077 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26457 Z= 0.149 Angle : 0.593 12.110 36129 Z= 0.298 Chirality : 0.045 0.231 4227 Planarity : 0.004 0.051 4575 Dihedral : 5.309 54.744 4665 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.33 % Allowed : 12.41 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3153 helix: 2.53 (0.21), residues: 630 sheet: 0.39 (0.20), residues: 627 loop : -1.07 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 353 HIS 0.004 0.001 HIS A1064 PHE 0.024 0.001 PHE A 32 TYR 0.022 0.001 TYR A 396 ARG 0.002 0.000 ARG A 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 48) link_NAG-ASN : angle 1.60773 ( 144) link_BETA1-4 : bond 0.00280 ( 9) link_BETA1-4 : angle 1.07618 ( 27) hydrogen bonds : bond 0.06330 ( 969) hydrogen bonds : angle 4.91050 ( 2853) link_BETA1-6 : bond 0.00281 ( 3) link_BETA1-6 : angle 1.28836 ( 9) SS BOND : bond 0.00206 ( 42) SS BOND : angle 1.54964 ( 84) covalent geometry : bond 0.00356 (26355) covalent geometry : angle 0.58094 (35865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14960.67 seconds wall clock time: 261 minutes 14.85 seconds (15674.85 seconds total)