Starting phenix.real_space_refine on Thu Mar 5 22:34:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r18_14234/03_2026/7r18_14234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r18_14234/03_2026/7r18_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_14234/03_2026/7r18_14234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r18_14234/03_2026/7r18_14234.map" model { file = "/net/cci-nas-00/data/ceres_data/7r18_14234/03_2026/7r18_14234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r18_14234/03_2026/7r18_14234.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.17, per 1000 atoms: 0.24 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 5.91 Time building geometry restraints manager: 2.96 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: 0.06 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.190 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (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 ARG 0.004 0.000 ARG A 905 TYR 0.018 0.002 TYR B 265 PHE 0.042 0.002 PHE B 906 TRP 0.036 0.002 TRP C 886 HIS 0.007 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00573 (26355) covalent geometry : angle 0.71318 (35865) SS BOND : bond 0.00322 ( 42) SS BOND : angle 1.77077 ( 84) hydrogen bonds : bond 0.13816 ( 969) hydrogen bonds : angle 6.58655 ( 2853) link_BETA1-4 : bond 0.00352 ( 9) link_BETA1-4 : angle 1.15652 ( 27) link_BETA1-6 : bond 0.00129 ( 3) link_BETA1-6 : angle 1.54259 ( 9) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 1.82637 ( 144) *********************** 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 : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.5354 time to fit residues: 204.0620 Evaluate side-chains 178 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 580 GLN B 957 GLN B1002 GLN B1010 GLN C 188 ASN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 580 GLN C 804 GLN C 957 GLN C1002 GLN C1010 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.182174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135744 restraints weight = 32745.406| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.30 r_work: 0.3111 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26457 Z= 0.174 Angle : 0.602 10.263 36129 Z= 0.311 Chirality : 0.046 0.179 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.811 54.457 4674 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.61 % Allowed : 5.92 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3153 helix: 2.44 (0.21), residues: 630 sheet: 0.47 (0.19), residues: 672 loop : -0.74 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.020 0.001 TYR C1067 PHE 0.026 0.002 PHE A 906 TRP 0.016 0.002 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00419 (26355) covalent geometry : angle 0.58980 (35865) SS BOND : bond 0.00208 ( 42) SS BOND : angle 1.28615 ( 84) hydrogen bonds : bond 0.07139 ( 969) hydrogen bonds : angle 5.48370 ( 2853) link_BETA1-4 : bond 0.00299 ( 9) link_BETA1-4 : angle 1.10371 ( 27) link_BETA1-6 : bond 0.00238 ( 3) link_BETA1-6 : angle 1.33100 ( 9) link_NAG-ASN : bond 0.00346 ( 48) link_NAG-ASN : angle 1.76358 ( 144) *********************** 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 231 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7067 (mttm) REVERT: A 196 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7688 (m-40) REVERT: A 378 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7649 (ttpp) REVERT: B 794 ILE cc_start: 0.8360 (mm) cc_final: 0.7613 (pp) REVERT: C 423 TYR cc_start: 0.8486 (t80) cc_final: 0.7899 (t80) REVERT: C 794 ILE cc_start: 0.8299 (mm) cc_final: 0.7468 (pp) outliers start: 45 outliers final: 18 residues processed: 212 average time/residue: 0.4784 time to fit residues: 123.5554 Evaluate side-chains 179 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 196 ASN 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 599 THR 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 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 1001 LEU 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 1001 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 210 optimal weight: 0.5980 chunk 265 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 316 optimal weight: 0.0470 chunk 117 optimal weight: 0.3980 chunk 41 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN A 957 GLN B 115 GLN B 394 ASN B 804 GLN B 957 GLN B1010 GLN C 115 GLN C 394 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.137868 restraints weight = 32851.184| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.30 r_work: 0.3180 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26457 Z= 0.119 Angle : 0.533 9.669 36129 Z= 0.274 Chirality : 0.044 0.179 4227 Planarity : 0.004 0.035 4575 Dihedral : 5.313 54.399 4667 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.54 % Allowed : 7.36 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3153 helix: 2.78 (0.21), residues: 612 sheet: 0.63 (0.19), residues: 675 loop : -0.85 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE C 906 TRP 0.010 0.001 TRP C 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00266 (26355) covalent geometry : angle 0.52274 (35865) SS BOND : bond 0.00165 ( 42) SS BOND : angle 0.89353 ( 84) hydrogen bonds : bond 0.05891 ( 969) hydrogen bonds : angle 5.12750 ( 2853) link_BETA1-4 : bond 0.00284 ( 9) link_BETA1-4 : angle 1.10107 ( 27) link_BETA1-6 : bond 0.00309 ( 3) link_BETA1-6 : angle 1.20492 ( 9) link_NAG-ASN : bond 0.00285 ( 48) link_NAG-ASN : angle 1.58047 ( 144) *********************** 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 223 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7907 (m-40) cc_final: 0.7699 (m110) REVERT: B 794 ILE cc_start: 0.8378 (mm) cc_final: 0.7693 (pp) REVERT: C 423 TYR cc_start: 0.8467 (t80) cc_final: 0.7970 (t80) REVERT: C 794 ILE cc_start: 0.8300 (mm) cc_final: 0.7499 (pp) REVERT: C 1119 ASN cc_start: 0.8017 (m-40) cc_final: 0.7751 (m110) outliers start: 43 outliers final: 18 residues processed: 202 average time/residue: 0.4690 time to fit residues: 116.0963 Evaluate side-chains 182 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 188 ASN 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 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 785 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 239 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 308 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 243 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 394 ASN A 957 GLN B 115 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.182475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135913 restraints weight = 32804.894| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.27 r_work: 0.3144 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26457 Z= 0.152 Angle : 0.558 11.143 36129 Z= 0.284 Chirality : 0.045 0.173 4227 Planarity : 0.004 0.036 4575 Dihedral : 5.223 55.112 4667 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.72 % Allowed : 8.72 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3153 helix: 2.77 (0.21), residues: 612 sheet: 0.56 (0.19), residues: 648 loop : -0.87 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 567 TYR 0.022 0.001 TYR A 396 PHE 0.017 0.001 PHE C 906 TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00363 (26355) covalent geometry : angle 0.54714 (35865) SS BOND : bond 0.00191 ( 42) SS BOND : angle 1.03428 ( 84) hydrogen bonds : bond 0.06415 ( 969) hydrogen bonds : angle 5.07793 ( 2853) link_BETA1-4 : bond 0.00253 ( 9) link_BETA1-4 : angle 1.12495 ( 27) link_BETA1-6 : bond 0.00217 ( 3) link_BETA1-6 : angle 1.26133 ( 9) link_NAG-ASN : bond 0.00291 ( 48) link_NAG-ASN : angle 1.57989 ( 144) *********************** 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 216 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7986 (m-40) cc_final: 0.7747 (m110) REVERT: B 794 ILE cc_start: 0.8386 (mm) cc_final: 0.7673 (pp) REVERT: C 140 PHE cc_start: 0.7701 (p90) cc_final: 0.7479 (p90) REVERT: C 392 PHE cc_start: 0.7625 (m-80) cc_final: 0.7309 (m-80) REVERT: C 423 TYR cc_start: 0.8530 (t80) cc_final: 0.7999 (t80) REVERT: C 564 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7820 (mm-40) REVERT: C 794 ILE cc_start: 0.8305 (mm) cc_final: 0.7479 (pp) outliers start: 48 outliers final: 26 residues processed: 202 average time/residue: 0.4503 time to fit residues: 112.1303 Evaluate side-chains 179 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 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 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 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 38 optimal weight: 5.9990 chunk 255 optimal weight: 20.0000 chunk 222 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 263 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 303 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B 422 ASN B1010 GLN C 30 ASN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.180830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134298 restraints weight = 32636.366| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.29 r_work: 0.3114 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26457 Z= 0.192 Angle : 0.599 11.056 36129 Z= 0.305 Chirality : 0.046 0.175 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.319 55.397 4667 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.76 % Allowed : 9.54 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3153 helix: 2.48 (0.21), residues: 630 sheet: 0.48 (0.19), residues: 651 loop : -0.95 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.022 0.001 TYR A 396 PHE 0.020 0.002 PHE A 906 TRP 0.012 0.001 TRP A 886 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00473 (26355) covalent geometry : angle 0.58615 (35865) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.47907 ( 84) hydrogen bonds : bond 0.07180 ( 969) hydrogen bonds : angle 5.14878 ( 2853) link_BETA1-4 : bond 0.00217 ( 9) link_BETA1-4 : angle 1.14123 ( 27) link_BETA1-6 : bond 0.00143 ( 3) link_BETA1-6 : angle 1.30885 ( 9) link_NAG-ASN : bond 0.00315 ( 48) link_NAG-ASN : angle 1.64261 ( 144) *********************** 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 220 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8788 (m-80) cc_final: 0.8530 (m-80) REVERT: B 564 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8065 (mm-40) REVERT: B 794 ILE cc_start: 0.8385 (mm) cc_final: 0.7669 (pp) REVERT: C 239 GLN cc_start: 0.7321 (mt0) cc_final: 0.7088 (mm110) REVERT: C 392 PHE cc_start: 0.7712 (m-80) cc_final: 0.7417 (m-80) REVERT: C 423 TYR cc_start: 0.8634 (t80) cc_final: 0.8111 (t80) REVERT: C 564 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7876 (mm-40) REVERT: C 794 ILE cc_start: 0.8376 (mm) cc_final: 0.7568 (pp) REVERT: C 1045 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7412 (tttm) outliers start: 49 outliers final: 30 residues processed: 207 average time/residue: 0.4371 time to fit residues: 111.6867 Evaluate side-chains 199 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 350 VAL 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 564 GLN 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 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 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 1045 LYS 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 205 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 257 optimal weight: 40.0000 chunk 163 optimal weight: 0.9980 chunk 65 optimal weight: 0.0020 chunk 112 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 238 optimal weight: 0.9980 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A1002 GLN B 957 GLN B1010 GLN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.182365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136910 restraints weight = 32727.714| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.30 r_work: 0.3148 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26457 Z= 0.137 Angle : 0.559 11.771 36129 Z= 0.282 Chirality : 0.044 0.177 4227 Planarity : 0.004 0.036 4575 Dihedral : 5.191 54.684 4667 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.87 % Allowed : 10.26 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3153 helix: 2.61 (0.21), residues: 630 sheet: 0.56 (0.19), residues: 663 loop : -0.95 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 102 TYR 0.019 0.001 TYR A 396 PHE 0.022 0.001 PHE B 32 TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00321 (26355) covalent geometry : angle 0.54697 (35865) SS BOND : bond 0.00190 ( 42) SS BOND : angle 1.35021 ( 84) hydrogen bonds : bond 0.06197 ( 969) hydrogen bonds : angle 4.95487 ( 2853) link_BETA1-4 : bond 0.00283 ( 9) link_BETA1-4 : angle 1.05217 ( 27) link_BETA1-6 : bond 0.00251 ( 3) link_BETA1-6 : angle 1.23775 ( 9) link_NAG-ASN : bond 0.00292 ( 48) link_NAG-ASN : angle 1.56766 ( 144) *********************** 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: 52 poor density : 169 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 396 TYR cc_start: 0.8760 (m-80) cc_final: 0.8538 (m-80) REVERT: A 1119 ASN cc_start: 0.7980 (m-40) cc_final: 0.7752 (m110) REVERT: B 529 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7726 (mmpt) REVERT: B 564 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (mm-40) REVERT: B 794 ILE cc_start: 0.8396 (mm) cc_final: 0.7685 (pp) REVERT: C 392 PHE cc_start: 0.7679 (m-80) cc_final: 0.7405 (m-80) REVERT: C 564 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7893 (mm-40) REVERT: C 794 ILE cc_start: 0.8353 (mm) cc_final: 0.7633 (pp) REVERT: C 1045 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7366 (tttm) outliers start: 52 outliers final: 30 residues processed: 207 average time/residue: 0.4142 time to fit residues: 106.8749 Evaluate side-chains 192 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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 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 350 VAL 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 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 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 1045 LYS 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 214 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 246 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 308 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 209 optimal weight: 1.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1010 GLN C 188 ASN ** C 422 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 = 0.4124 r_free = 0.4124 target = 0.181621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134854 restraints weight = 32544.973| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.27 r_work: 0.3123 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26457 Z= 0.159 Angle : 0.580 11.713 36129 Z= 0.293 Chirality : 0.045 0.182 4227 Planarity : 0.004 0.040 4575 Dihedral : 5.188 54.826 4665 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.69 % Allowed : 11.02 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3153 helix: 2.57 (0.21), residues: 630 sheet: 0.50 (0.19), residues: 642 loop : -0.99 (0.13), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.020 0.001 TYR B 396 PHE 0.019 0.001 PHE B 140 TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00384 (26355) covalent geometry : angle 0.56736 (35865) SS BOND : bond 0.00207 ( 42) SS BOND : angle 1.52917 ( 84) hydrogen bonds : bond 0.06530 ( 969) hydrogen bonds : angle 4.97171 ( 2853) link_BETA1-4 : bond 0.00259 ( 9) link_BETA1-4 : angle 1.08111 ( 27) link_BETA1-6 : bond 0.00201 ( 3) link_BETA1-6 : angle 1.27501 ( 9) link_NAG-ASN : bond 0.00292 ( 48) link_NAG-ASN : angle 1.58060 ( 144) *********************** 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 212 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: B 564 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (mm-40) REVERT: B 794 ILE cc_start: 0.8392 (mm) cc_final: 0.7667 (pp) REVERT: C 239 GLN cc_start: 0.7244 (mt0) cc_final: 0.6899 (mm110) REVERT: C 392 PHE cc_start: 0.7700 (m-80) cc_final: 0.7420 (m-80) REVERT: C 423 TYR cc_start: 0.8446 (t80) cc_final: 0.8039 (t80) REVERT: C 564 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: C 794 ILE cc_start: 0.8347 (mm) cc_final: 0.7616 (pp) REVERT: C 1045 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7459 (tttm) outliers start: 47 outliers final: 32 residues processed: 198 average time/residue: 0.4242 time to fit residues: 103.9155 Evaluate side-chains 192 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 697 MET 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 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 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 1045 LYS 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 175 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1010 GLN C 188 ASN ** C 422 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 = 0.4122 r_free = 0.4122 target = 0.181462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.136549 restraints weight = 32662.408| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.27 r_work: 0.3144 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26457 Z= 0.163 Angle : 0.587 11.915 36129 Z= 0.295 Chirality : 0.045 0.195 4227 Planarity : 0.004 0.039 4575 Dihedral : 5.188 54.809 4665 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.69 % Allowed : 11.30 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3153 helix: 2.63 (0.21), residues: 612 sheet: 0.48 (0.19), residues: 642 loop : -1.04 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.001 PHE A 32 TRP 0.010 0.001 TRP C 152 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00395 (26355) covalent geometry : angle 0.57570 (35865) SS BOND : bond 0.00217 ( 42) SS BOND : angle 1.33574 ( 84) hydrogen bonds : bond 0.06579 ( 969) hydrogen bonds : angle 4.95548 ( 2853) link_BETA1-4 : bond 0.00255 ( 9) link_BETA1-4 : angle 1.08443 ( 27) link_BETA1-6 : bond 0.00198 ( 3) link_BETA1-6 : angle 1.27481 ( 9) link_NAG-ASN : bond 0.00297 ( 48) link_NAG-ASN : angle 1.59083 ( 144) *********************** 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 208 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 564 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8117 (mm-40) REVERT: B 794 ILE cc_start: 0.8393 (mm) cc_final: 0.7699 (pp) REVERT: C 392 PHE cc_start: 0.7747 (m-80) cc_final: 0.7502 (m-80) REVERT: C 423 TYR cc_start: 0.8506 (t80) cc_final: 0.8092 (t80) REVERT: C 564 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7874 (mm-40) REVERT: C 794 ILE cc_start: 0.8372 (mm) cc_final: 0.7799 (pp) REVERT: C 1045 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7434 (tttm) outliers start: 47 outliers final: 33 residues processed: 195 average time/residue: 0.4008 time to fit residues: 98.0651 Evaluate side-chains 195 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 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 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 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 1045 LYS 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 301 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 287 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1002 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.4139 r_free = 0.4139 target = 0.183133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138053 restraints weight = 32590.518| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.33 r_work: 0.3160 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2035 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= 0.122 Angle : 0.559 12.018 36129 Z= 0.278 Chirality : 0.044 0.188 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.068 54.418 4665 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.22 % Allowed : 12.02 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3153 helix: 2.81 (0.21), residues: 612 sheet: 0.59 (0.19), residues: 642 loop : -0.99 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 567 TYR 0.023 0.001 TYR B 396 PHE 0.013 0.001 PHE A 400 TRP 0.011 0.001 TRP B 152 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00283 (26355) covalent geometry : angle 0.54928 (35865) SS BOND : bond 0.00169 ( 42) SS BOND : angle 1.07433 ( 84) hydrogen bonds : bond 0.05676 ( 969) hydrogen bonds : angle 4.77464 ( 2853) link_BETA1-4 : bond 0.00308 ( 9) link_BETA1-4 : angle 1.03561 ( 27) link_BETA1-6 : bond 0.00280 ( 3) link_BETA1-6 : angle 1.22814 ( 9) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 1.52327 ( 144) *********************** 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 200 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7906 (m-40) cc_final: 0.7695 (m110) REVERT: B 378 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7613 (tttp) REVERT: B 564 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (mm-40) REVERT: B 794 ILE cc_start: 0.8373 (mm) cc_final: 0.7672 (pp) REVERT: C 392 PHE cc_start: 0.7688 (m-80) cc_final: 0.7412 (m-80) REVERT: C 423 TYR cc_start: 0.8459 (t80) cc_final: 0.8084 (t80) REVERT: C 564 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7917 (mm-40) REVERT: C 794 ILE cc_start: 0.8361 (mm) cc_final: 0.7782 (pp) REVERT: C 1119 ASN cc_start: 0.7962 (m-40) cc_final: 0.7711 (m110) outliers start: 34 outliers final: 25 residues processed: 187 average time/residue: 0.4118 time to fit residues: 95.9936 Evaluate side-chains 181 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 878 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 576 VAL 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 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 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 159 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 206 optimal weight: 0.0770 chunk 260 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1002 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 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 = 0.4135 r_free = 0.4135 target = 0.182688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136948 restraints weight = 32550.042| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.22 r_work: 0.3159 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26457 Z= 0.132 Angle : 0.572 11.978 36129 Z= 0.285 Chirality : 0.044 0.180 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.066 54.661 4665 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.08 % Allowed : 12.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3153 helix: 2.80 (0.21), residues: 612 sheet: 0.60 (0.19), residues: 642 loop : -1.00 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.018 0.001 TYR C1067 PHE 0.013 0.001 PHE B 400 TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00313 (26355) covalent geometry : angle 0.55998 (35865) SS BOND : bond 0.00183 ( 42) SS BOND : angle 1.51800 ( 84) hydrogen bonds : bond 0.05865 ( 969) hydrogen bonds : angle 4.78213 ( 2853) link_BETA1-4 : bond 0.00299 ( 9) link_BETA1-4 : angle 1.05043 ( 27) link_BETA1-6 : bond 0.00284 ( 3) link_BETA1-6 : angle 1.25588 ( 9) link_NAG-ASN : bond 0.00274 ( 48) link_NAG-ASN : angle 1.52427 ( 144) ********************** 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 187 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7943 (m-40) cc_final: 0.7675 (m110) REVERT: B 378 LYS cc_start: 0.7898 (ptmm) cc_final: 0.7525 (tttp) REVERT: B 564 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8132 (mm-40) REVERT: B 794 ILE cc_start: 0.8371 (mm) cc_final: 0.7652 (pp) REVERT: C 392 PHE cc_start: 0.7651 (m-80) cc_final: 0.7381 (m-80) REVERT: C 423 TYR cc_start: 0.8466 (t80) cc_final: 0.8080 (t80) REVERT: C 564 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7863 (mm-40) REVERT: C 794 ILE cc_start: 0.8340 (mm) cc_final: 0.7776 (pp) REVERT: C 1119 ASN cc_start: 0.8013 (m-40) cc_final: 0.7756 (m110) outliers start: 30 outliers final: 24 residues processed: 178 average time/residue: 0.4217 time to fit residues: 92.6079 Evaluate side-chains 183 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 878 LEU Chi-restraints excluded: chain B residue 51 THR 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 576 VAL 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 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 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 169 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 270 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1010 GLN C 188 ASN ** C 422 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 = 0.4137 r_free = 0.4137 target = 0.182796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136541 restraints weight = 32499.737| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.30 r_work: 0.3153 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2145 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= 0.128 Angle : 0.566 12.064 36129 Z= 0.282 Chirality : 0.044 0.168 4227 Planarity : 0.004 0.037 4575 Dihedral : 5.039 54.631 4665 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.15 % Allowed : 12.56 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3153 helix: 2.82 (0.21), residues: 612 sheet: 0.62 (0.19), residues: 642 loop : -1.00 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.022 0.001 TYR A 396 PHE 0.025 0.001 PHE A 32 TRP 0.012 0.001 TRP A 152 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00300 (26355) covalent geometry : angle 0.55588 (35865) SS BOND : bond 0.00175 ( 42) SS BOND : angle 1.30175 ( 84) hydrogen bonds : bond 0.05736 ( 969) hydrogen bonds : angle 4.74257 ( 2853) link_BETA1-4 : bond 0.00295 ( 9) link_BETA1-4 : angle 1.03977 ( 27) link_BETA1-6 : bond 0.00256 ( 3) link_BETA1-6 : angle 1.23080 ( 9) link_NAG-ASN : bond 0.00271 ( 48) link_NAG-ASN : angle 1.49762 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6568.50 seconds wall clock time: 112 minutes 59.45 seconds (6779.45 seconds total)