Starting phenix.real_space_refine on Sun Jul 5 05:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r18_14234/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.map" model { file = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_2026/7r18_14234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r18_14234/07_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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 13 Time building chain proxies: 5.16, per 1000 atoms: 0.20 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: 2.29 Conformation dependent library (CDL) restraints added in 909.0 milliseconds 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: 0.90 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: 4.51 Time building geometry restraints manager: 2.93 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: 14258 17.62 - 35.24: 844 35.24 - 52.86: 102 52.86 - 70.48: 15 70.48 - 88.10: 6 Dihedral angle restraints: 15225 sinusoidal: 5952 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 15222 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: 0.04 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: 3.710 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.400 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 11.037 74.888 9135 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/Z covalent geometry : bond 0.00573 / 0.30 (26355) covalent geometry : angle 0.71318 / 0.42 (35865) SS BOND : bond 0.00322 / 0.22 ( 42) SS BOND : angle 1.77077 / 1.23 ( 84) hydrogen bonds : bond 0.13816 / 9.28 ( 969) hydrogen bonds : angle 6.58655 / 4.63 ( 2853) link_BETA1-4 : bond 0.00352 / 0.17 ( 9) link_BETA1-4 : angle 1.15652 / 0.73 ( 27) link_BETA1-6 : bond 0.00129 / 0.06 ( 3) link_BETA1-6 : angle 1.54259 / 0.98 ( 9) link_NAG-ASN : bond 0.00346 / 0.23 ( 48) link_NAG-ASN : angle 1.82637 / 1.31 ( 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 : 1.027 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: 0.5153 time to fit residues: 198.2570 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 : 0.979 ------------------------------------------------------------------------------- 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... 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 = 0.182267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134911 restraints weight = 32768.391| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.16 r_work: 0.3131 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1125 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= 0.174 Angle : 0.604 10.287 36129 Z= 0.312 Chirality : 0.046 0.176 4227 Planarity : 0.004 0.037 4575 Dihedral : 4.615 46.173 3426 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.54 % Allowed : 5.96 % Favored : 92.50 % 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: 2.45 (0.21), residues: 630 sheet: 0.46 (0.19), residues: 684 loop : -0.76 (0.13), residues: 1839 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 0.001 TRP A 886 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (26355) covalent geometry : angle 0.59188 / 0.31 (35865) SS BOND : bond 0.00210 / 0.14 ( 42) SS BOND : angle 1.30385 / 0.91 ( 84) hydrogen bonds : bond 0.07125 / 4.70 ( 969) hydrogen bonds : angle 5.47779 / 3.79 ( 2853) link_BETA1-4 : bond 0.00272 / 0.14 ( 9) link_BETA1-4 : angle 0.96676 / 0.62 ( 27) link_BETA1-6 : bond 0.00203 / 0.10 ( 3) link_BETA1-6 : angle 1.48951 / 0.92 ( 9) link_NAG-ASN : bond 0.00326 / 0.21 ( 48) link_NAG-ASN : angle 1.75390 / 1.29 ( 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 226 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7053 (mttm) REVERT: A 196 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7705 (m-40) REVERT: A 378 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7652 (ttpp) REVERT: B 794 ILE cc_start: 0.8375 (mm) cc_final: 0.7653 (pp) REVERT: C 423 TYR cc_start: 0.8474 (t80) cc_final: 0.7897 (t80) REVERT: C 794 ILE cc_start: 0.8284 (mm) cc_final: 0.7465 (pp) outliers start: 43 outliers final: 16 residues processed: 206 average time/residue: 0.4877 time to fit residues: 122.7253 Evaluate side-chains 175 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 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: 0.0050 chunk 265 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 316 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 394 ASN A 957 GLN B 115 GLN B 394 ASN B 804 GLN B 957 GLN B1010 GLN C 394 ASN C 957 GLN C1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.184740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139069 restraints weight = 32938.873| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.32 r_work: 0.3183 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26457 Z= 0.108 Angle : 0.522 9.641 36129 Z= 0.267 Chirality : 0.043 0.186 4227 Planarity : 0.004 0.034 4575 Dihedral : 4.147 25.684 3419 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.47 % Allowed : 7.18 % Favored : 91.35 % 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: 0.42 (0.14), residues: 3153 helix: 2.86 (0.21), residues: 612 sheet: 0.71 (0.19), residues: 669 loop : -0.81 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 357 TYR 0.018 0.001 TYR B 396 PHE 0.014 0.001 PHE C 906 TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (26355) covalent geometry : angle 0.51255 / 0.27 (35865) SS BOND : bond 0.00163 / 0.11 ( 42) SS BOND : angle 0.79956 / 0.55 ( 84) hydrogen bonds : bond 0.05510 / 3.64 ( 969) hydrogen bonds : angle 5.06301 / 3.50 ( 2853) link_BETA1-4 : bond 0.00378 / 0.19 ( 9) link_BETA1-4 : angle 0.90816 / 0.58 ( 27) link_BETA1-6 : bond 0.00379 / 0.19 ( 3) link_BETA1-6 : angle 1.16811 / 0.74 ( 9) link_NAG-ASN : bond 0.00303 / 0.20 ( 48) link_NAG-ASN : angle 1.50707 / 1.11 ( 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 228 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7876 (m-40) cc_final: 0.7607 (m110) REVERT: B 794 ILE cc_start: 0.8359 (mm) cc_final: 0.7636 (pp) REVERT: C 239 GLN cc_start: 0.7291 (mt0) cc_final: 0.6969 (mt0) REVERT: C 564 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7772 (mm-40) REVERT: C 794 ILE cc_start: 0.8344 (mm) cc_final: 0.7507 (pp) REVERT: C 904 TYR cc_start: 0.8374 (m-10) cc_final: 0.7904 (m-10) REVERT: C 1119 ASN cc_start: 0.7998 (m-40) cc_final: 0.7740 (m110) outliers start: 41 outliers final: 16 residues processed: 209 average time/residue: 0.4459 time to fit residues: 114.8223 Evaluate side-chains 179 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 239 optimal weight: 0.0170 chunk 93 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 115 GLN B 188 ASN B 422 ASN B1010 GLN C 115 GLN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.180988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.133293 restraints weight = 32778.846| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.23 r_work: 0.3113 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 26457 Z= 0.193 Angle : 0.597 11.620 36129 Z= 0.305 Chirality : 0.046 0.171 4227 Planarity : 0.004 0.037 4575 Dihedral : 4.310 24.282 3419 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 9.01 % Favored : 89.34 % 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: 2.57 (0.21), residues: 630 sheet: 0.50 (0.19), residues: 663 loop : -0.91 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.022 0.002 TYR A 396 PHE 0.023 0.002 PHE C 906 TRP 0.014 0.002 TRP A 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.19 (26355) covalent geometry : angle 0.58697 / 0.30 (35865) SS BOND : bond 0.00242 / 0.17 ( 42) SS BOND : angle 1.22204 / 0.85 ( 84) hydrogen bonds : bond 0.07215 / 4.75 ( 969) hydrogen bonds : angle 5.18173 / 3.58 ( 2853) link_BETA1-4 : bond 0.00240 / 0.11 ( 9) link_BETA1-4 : angle 1.02268 / 0.65 ( 27) link_BETA1-6 : bond 0.00157 / 0.08 ( 3) link_BETA1-6 : angle 1.31780 / 0.80 ( 9) link_NAG-ASN : bond 0.00307 / 0.20 ( 48) link_NAG-ASN : angle 1.54703 / 1.16 ( 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: 46 poor density : 170 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7294 (p0) cc_final: 0.7083 (p0) REVERT: B 794 ILE cc_start: 0.8411 (mm) cc_final: 0.7693 (pp) REVERT: C 392 PHE cc_start: 0.7686 (m-80) cc_final: 0.7363 (m-80) REVERT: C 423 TYR cc_start: 0.8587 (t80) cc_final: 0.8027 (t80) REVERT: C 794 ILE cc_start: 0.8330 (mm) cc_final: 0.7500 (pp) outliers start: 46 outliers final: 27 residues processed: 205 average time/residue: 0.4249 time to fit residues: 108.9313 Evaluate side-chains 188 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 222 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 9 optimal weight: 7.9990 chunk 303 optimal weight: 0.5980 chunk 152 optimal weight: 40.0000 chunk 113 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.181333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135801 restraints weight = 32658.156| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.26 r_work: 0.3133 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26457 Z= 0.169 Angle : 0.577 11.098 36129 Z= 0.294 Chirality : 0.045 0.175 4227 Planarity : 0.004 0.039 4575 Dihedral : 4.274 24.759 3419 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.44 % Allowed : 10.15 % Favored : 88.41 % 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: 0.16 (0.14), residues: 3153 helix: 2.52 (0.21), residues: 630 sheet: 0.52 (0.19), residues: 678 loop : -0.97 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.021 0.001 TYR A 396 PHE 0.021 0.002 PHE B 32 TRP 0.010 0.001 TRP C 353 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (26355) covalent geometry : angle 0.56577 / 0.29 (35865) SS BOND : bond 0.00206 / 0.14 ( 42) SS BOND : angle 1.33832 / 0.89 ( 84) hydrogen bonds : bond 0.06737 / 4.44 ( 969) hydrogen bonds : angle 5.08240 / 3.52 ( 2853) link_BETA1-4 : bond 0.00243 / 0.12 ( 9) link_BETA1-4 : angle 0.99069 / 0.63 ( 27) link_BETA1-6 : bond 0.00168 / 0.08 ( 3) link_BETA1-6 : angle 1.26125 / 0.77 ( 9) link_NAG-ASN : bond 0.00310 / 0.20 ( 48) link_NAG-ASN : angle 1.52896 / 1.14 ( 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 212 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7304 (p0) cc_final: 0.6993 (p0) REVERT: A 396 TYR cc_start: 0.8760 (m-80) cc_final: 0.8476 (m-80) REVERT: A 529 LYS cc_start: 0.7908 (mmpt) cc_final: 0.7638 (mmpt) REVERT: B 529 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7711 (mmpt) REVERT: B 794 ILE cc_start: 0.8384 (mm) cc_final: 0.7673 (pp) REVERT: C 392 PHE cc_start: 0.7705 (m-80) cc_final: 0.7430 (m-80) REVERT: C 423 TYR cc_start: 0.8570 (t80) cc_final: 0.8077 (t80) REVERT: C 794 ILE cc_start: 0.8377 (mm) cc_final: 0.7571 (pp) REVERT: C 1045 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7371 (tttm) outliers start: 40 outliers final: 29 residues processed: 201 average time/residue: 0.4567 time to fit residues: 113.3932 Evaluate side-chains 191 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 758 SER 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: 0.9990 chunk 133 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 257 optimal weight: 40.0000 chunk 163 optimal weight: 0.6980 chunk 65 optimal weight: 0.0970 chunk 112 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 957 GLN B1010 GLN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.181917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135977 restraints weight = 32762.665| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.49 r_work: 0.3086 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1780 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= 0.148 Angle : 0.564 11.578 36129 Z= 0.286 Chirality : 0.045 0.181 4227 Planarity : 0.004 0.038 4575 Dihedral : 4.214 25.509 3419 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.79 % Allowed : 10.58 % Favored : 87.62 % 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: 0.19 (0.14), residues: 3153 helix: 2.58 (0.21), residues: 630 sheet: 0.57 (0.19), residues: 663 loop : -0.96 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 567 TYR 0.021 0.001 TYR B 396 PHE 0.027 0.001 PHE C 140 TRP 0.009 0.001 TRP B 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (26355) covalent geometry : angle 0.55268 / 0.28 (35865) SS BOND : bond 0.00211 / 0.14 ( 42) SS BOND : angle 1.36529 / 1.07 ( 84) hydrogen bonds : bond 0.06412 / 4.23 ( 969) hydrogen bonds : angle 4.99201 / 3.45 ( 2853) link_BETA1-4 : bond 0.00274 / 0.13 ( 9) link_BETA1-4 : angle 0.98678 / 0.63 ( 27) link_BETA1-6 : bond 0.00172 / 0.09 ( 3) link_BETA1-6 : angle 1.25211 / 0.77 ( 9) link_NAG-ASN : bond 0.00290 / 0.19 ( 48) link_NAG-ASN : angle 1.51266 / 1.13 ( 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 219 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7294 (p0) cc_final: 0.6976 (p0) REVERT: A 396 TYR cc_start: 0.8641 (m-80) cc_final: 0.8360 (m-80) REVERT: A 529 LYS cc_start: 0.7965 (mmpt) cc_final: 0.7624 (mmpt) REVERT: A 1119 ASN cc_start: 0.8118 (m-40) cc_final: 0.7897 (m110) REVERT: B 529 LYS cc_start: 0.8053 (mmpt) cc_final: 0.7669 (mmpt) REVERT: B 564 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (mm-40) REVERT: B 794 ILE cc_start: 0.8383 (mm) cc_final: 0.7586 (pp) REVERT: C 392 PHE cc_start: 0.7632 (m-80) cc_final: 0.7320 (m-80) REVERT: C 423 TYR cc_start: 0.8624 (t80) cc_final: 0.8402 (t80) REVERT: C 794 ILE cc_start: 0.8372 (mm) cc_final: 0.7582 (pp) REVERT: C 1045 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7469 (tttm) outliers start: 50 outliers final: 28 residues processed: 206 average time/residue: 0.4292 time to fit residues: 110.4594 Evaluate side-chains 185 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.7980 chunk 14 optimal weight: 10.0000 chunk 246 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 308 optimal weight: 0.0470 chunk 134 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.182970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138570 restraints weight = 32606.715| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.37 r_work: 0.3151 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26457 Z= 0.127 Angle : 0.552 11.721 36129 Z= 0.278 Chirality : 0.044 0.184 4227 Planarity : 0.004 0.037 4575 Dihedral : 4.073 25.857 3417 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.61 % Allowed : 11.41 % Favored : 86.98 % 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: 2.76 (0.21), residues: 612 sheet: 0.58 (0.19), residues: 645 loop : -0.98 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 567 TYR 0.018 0.001 TYR A 396 PHE 0.021 0.001 PHE A 32 TRP 0.011 0.001 TRP B 353 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (26355) covalent geometry : angle 0.54109 / 0.28 (35865) SS BOND : bond 0.00184 / 0.13 ( 42) SS BOND : angle 1.33877 / 1.12 ( 84) hydrogen bonds : bond 0.05854 / 3.86 ( 969) hydrogen bonds : angle 4.85493 / 3.35 ( 2853) link_BETA1-4 : bond 0.00304 / 0.14 ( 9) link_BETA1-4 : angle 0.96480 / 0.61 ( 27) link_BETA1-6 : bond 0.00145 / 0.07 ( 3) link_BETA1-6 : angle 1.15059 / 0.69 ( 9) link_NAG-ASN : bond 0.00279 / 0.18 ( 48) link_NAG-ASN : angle 1.46067 / 1.08 ( 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 213 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7465 (p0) cc_final: 0.7164 (p0) REVERT: A 396 TYR cc_start: 0.8749 (m-80) cc_final: 0.8498 (m-80) REVERT: A 529 LYS cc_start: 0.7890 (mmpt) cc_final: 0.7635 (mmpt) REVERT: A 1119 ASN cc_start: 0.7952 (m-40) cc_final: 0.7743 (m110) REVERT: B 177 MET cc_start: 0.4814 (pmt) cc_final: 0.4583 (pmm) REVERT: B 529 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7730 (mmpt) REVERT: B 564 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: B 794 ILE cc_start: 0.8392 (mm) cc_final: 0.7672 (pp) REVERT: C 392 PHE cc_start: 0.7691 (m-80) cc_final: 0.7412 (m-80) REVERT: C 564 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: C 794 ILE cc_start: 0.8359 (mm) cc_final: 0.7636 (pp) REVERT: C 1119 ASN cc_start: 0.7999 (m-40) cc_final: 0.7716 (m110) outliers start: 45 outliers final: 28 residues processed: 197 average time/residue: 0.4310 time to fit residues: 106.3383 Evaluate side-chains 191 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 175 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 957 GLN B 188 ASN B1010 GLN C 30 ASN C 188 ASN C 422 ASN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133724 restraints weight = 32701.584| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.50 r_work: 0.3052 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26457 Z= 0.219 Angle : 0.631 11.913 36129 Z= 0.319 Chirality : 0.047 0.183 4227 Planarity : 0.004 0.046 4575 Dihedral : 4.330 26.428 3417 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.69 % Allowed : 11.59 % Favored : 86.72 % 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: -0.01 (0.14), residues: 3153 helix: 2.42 (0.21), residues: 630 sheet: 0.40 (0.19), residues: 630 loop : -1.05 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 905 TYR 0.020 0.002 TYR C1067 PHE 0.022 0.002 PHE A1121 TRP 0.016 0.002 TRP B 353 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.22 (26355) covalent geometry : angle 0.61891 / 0.32 (35865) SS BOND : bond 0.00319 / 0.23 ( 42) SS BOND : angle 1.73877 / 1.27 ( 84) hydrogen bonds : bond 0.07505 / 4.94 ( 969) hydrogen bonds : angle 5.09765 / 3.51 ( 2853) link_BETA1-4 : bond 0.00230 / 0.11 ( 9) link_BETA1-4 : angle 1.11370 / 0.71 ( 27) link_BETA1-6 : bond 0.00084 / 0.04 ( 3) link_BETA1-6 : angle 1.30121 / 0.79 ( 9) link_NAG-ASN : bond 0.00332 / 0.23 ( 48) link_NAG-ASN : angle 1.57892 / 1.18 ( 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 210 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7448 (p0) cc_final: 0.7091 (p0) REVERT: A 396 TYR cc_start: 0.8646 (m-80) cc_final: 0.8365 (m-80) REVERT: A 529 LYS cc_start: 0.7960 (mmpt) cc_final: 0.7625 (mmpt) REVERT: B 794 ILE cc_start: 0.8427 (mm) cc_final: 0.7659 (pp) REVERT: C 239 GLN cc_start: 0.7314 (mt0) cc_final: 0.6950 (mm110) REVERT: C 392 PHE cc_start: 0.7700 (m-80) cc_final: 0.7390 (m-80) REVERT: C 423 TYR cc_start: 0.8433 (t80) cc_final: 0.8001 (t80) REVERT: C 564 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: C 794 ILE cc_start: 0.8405 (mm) cc_final: 0.7753 (pp) REVERT: C 1045 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7513 (tttm) outliers start: 47 outliers final: 31 residues processed: 198 average time/residue: 0.4425 time to fit residues: 108.1177 Evaluate side-chains 193 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 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 1045 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 301 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 191 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN A1002 GLN B 188 ASN B 957 GLN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137343 restraints weight = 32535.976| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.36 r_work: 0.3154 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26457 Z= 0.121 Angle : 0.560 12.131 36129 Z= 0.279 Chirality : 0.043 0.175 4227 Planarity : 0.004 0.037 4575 Dihedral : 4.074 24.456 3417 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.26 % Allowed : 12.27 % 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: 0.14 (0.14), residues: 3153 helix: 2.73 (0.21), residues: 612 sheet: 0.58 (0.20), residues: 636 loop : -1.03 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 567 TYR 0.018 0.001 TYR C1067 PHE 0.022 0.001 PHE A 32 TRP 0.011 0.001 TRP B 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26355) covalent geometry : angle 0.55020 / 0.28 (35865) SS BOND : bond 0.00170 / 0.12 ( 42) SS BOND : angle 1.23828 / 0.91 ( 84) hydrogen bonds : bond 0.05766 / 3.81 ( 969) hydrogen bonds : angle 4.81589 / 3.32 ( 2853) link_BETA1-4 : bond 0.00331 / 0.16 ( 9) link_BETA1-4 : angle 0.96010 / 0.61 ( 27) link_BETA1-6 : bond 0.00221 / 0.11 ( 3) link_BETA1-6 : angle 1.23366 / 0.76 ( 9) link_NAG-ASN : bond 0.00280 / 0.19 ( 48) link_NAG-ASN : angle 1.46953 / 1.08 ( 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 198 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7599 (p0) cc_final: 0.7357 (p0) REVERT: A 396 TYR cc_start: 0.8707 (m-80) cc_final: 0.8500 (m-80) REVERT: A 1119 ASN cc_start: 0.7956 (m-40) cc_final: 0.7735 (m110) REVERT: B 177 MET cc_start: 0.4977 (pmt) cc_final: 0.4677 (pmm) REVERT: B 378 LYS cc_start: 0.7896 (ptmm) cc_final: 0.7533 (tttp) REVERT: B 564 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: B 794 ILE cc_start: 0.8391 (mm) cc_final: 0.7692 (pp) REVERT: C 392 PHE cc_start: 0.7705 (m-80) cc_final: 0.7416 (m-80) REVERT: C 423 TYR cc_start: 0.8459 (t80) cc_final: 0.8100 (t80) REVERT: C 564 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: C 794 ILE cc_start: 0.8380 (mm) cc_final: 0.7797 (pp) REVERT: C 1119 ASN cc_start: 0.8011 (m-40) cc_final: 0.7727 (m110) outliers start: 35 outliers final: 29 residues processed: 186 average time/residue: 0.4430 time to fit residues: 102.6246 Evaluate side-chains 188 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 599 THR 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 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR 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: 3.9990 chunk 27 optimal weight: 0.6980 chunk 299 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 313 optimal weight: 0.8980 chunk 206 optimal weight: 0.0670 chunk 260 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN B 188 ASN B1010 GLN C 188 ASN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136999 restraints weight = 32593.198| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.29 r_work: 0.3164 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2104 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= 0.131 Angle : 0.568 12.014 36129 Z= 0.283 Chirality : 0.044 0.167 4227 Planarity : 0.004 0.038 4575 Dihedral : 4.036 23.474 3417 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.22 % Allowed : 12.49 % 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: 0.16 (0.15), residues: 3153 helix: 2.79 (0.21), residues: 612 sheet: 0.56 (0.19), residues: 642 loop : -1.03 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.020 0.001 TYR B 396 PHE 0.019 0.001 PHE C 32 TRP 0.012 0.001 TRP A 152 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (26355) covalent geometry : angle 0.55867 / 0.28 (35865) SS BOND : bond 0.00183 / 0.13 ( 42) SS BOND : angle 1.20312 / 0.88 ( 84) hydrogen bonds : bond 0.05894 / 3.89 ( 969) hydrogen bonds : angle 4.77643 / 3.29 ( 2853) link_BETA1-4 : bond 0.00282 / 0.14 ( 9) link_BETA1-4 : angle 0.98793 / 0.63 ( 27) link_BETA1-6 : bond 0.00219 / 0.11 ( 3) link_BETA1-6 : angle 1.23047 / 0.76 ( 9) link_NAG-ASN : bond 0.00269 / 0.18 ( 48) link_NAG-ASN : angle 1.45554 / 1.08 ( 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 192 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 1119 ASN cc_start: 0.7939 (m-40) cc_final: 0.7737 (m110) REVERT: B 564 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8105 (mm-40) REVERT: B 794 ILE cc_start: 0.8371 (mm) cc_final: 0.7678 (pp) REVERT: C 392 PHE cc_start: 0.7688 (m-80) cc_final: 0.7419 (m-80) REVERT: C 423 TYR cc_start: 0.8481 (t80) cc_final: 0.8143 (t80) REVERT: C 546 LEU cc_start: 0.7198 (tt) cc_final: 0.6681 (pp) REVERT: C 564 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7879 (mm-40) REVERT: C 794 ILE cc_start: 0.8368 (mm) cc_final: 0.7793 (pp) REVERT: C 1119 ASN cc_start: 0.7937 (m-40) cc_final: 0.7676 (m110) outliers start: 34 outliers final: 28 residues processed: 181 average time/residue: 0.4386 time to fit residues: 98.9560 Evaluate side-chains 183 residues out of total 2787 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 599 THR 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 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 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 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 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: 1.9990 chunk 134 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 270 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 188 ASN B1010 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132395 restraints weight = 32574.409| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.38 r_work: 0.3105 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26457 Z= 0.210 Angle : 0.628 12.222 36129 Z= 0.316 Chirality : 0.047 0.166 4227 Planarity : 0.004 0.044 4575 Dihedral : 4.249 23.741 3417 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.18 % Allowed : 12.59 % Favored : 86.22 % 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: -0.05 (0.14), residues: 3153 helix: 2.52 (0.21), residues: 612 sheet: 0.34 (0.20), residues: 630 loop : -1.08 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.019 0.001 TYR C1067 PHE 0.023 0.002 PHE A 32 TRP 0.009 0.001 TRP B 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 (26355) covalent geometry : angle 0.61680 / 0.31 (35865) SS BOND : bond 0.00279 / 0.19 ( 42) SS BOND : angle 1.66836 / 1.18 ( 84) hydrogen bonds : bond 0.07217 / 4.76 ( 969) hydrogen bonds : angle 4.98906 / 3.44 ( 2853) link_BETA1-4 : bond 0.00238 / 0.11 ( 9) link_BETA1-4 : angle 1.09549 / 0.70 ( 27) link_BETA1-6 : bond 0.00105 / 0.05 ( 3) link_BETA1-6 : angle 1.28151 / 0.79 ( 9) link_NAG-ASN : bond 0.00318 / 0.21 ( 48) link_NAG-ASN : angle 1.54465 / 1.15 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6878.26 seconds wall clock time: 118 minutes 52.14 seconds (7132.14 seconds total)