Starting phenix.real_space_refine on Mon Aug 25 06:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ios_35622/08_2025/8ios_35622.map" } resolution = 2.5 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= 0.000 sd= 0.016 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 16371 2.51 5 N 4215 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25695 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "B" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "C" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8313 Classifications: {'peptide': 1063} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.19, per 1000 atoms: 0.28 Number of scatterers: 25695 At special positions: 0 Unit cell: (137.685, 131.655, 165.825, 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 4995 8.00 N 4215 7.00 C 16371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.04 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=2.03 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 A 840 " - pdb=" SG CYS A 851 " 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 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=2.03 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=2.04 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=2.03 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 B 840 " - pdb=" SG CYS B 851 " 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 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=2.03 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=2.04 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=2.03 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 C 840 " - pdb=" SG CYS C 851 " 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 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1098 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5982 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 51 sheets defined 26.0% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 155 through 159 removed outlier: 4.511A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.933A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.625A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.548A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.708A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.508A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 848 through 855 removed outlier: 3.659A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.138A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.590A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.892A 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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.163A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 155 through 159 removed outlier: 4.510A pdb=" N ARG B 158 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.934A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.625A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.549A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.707A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.509A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.659A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.589A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.892A 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 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 155 through 159 removed outlier: 4.511A pdb=" N ARG C 158 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.934A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.624A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.549A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.708A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.729A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.509A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.660A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.891A 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 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.164A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.624A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 removed outlier: 4.336A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.649A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.560A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.178A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.019A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.632A 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 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.995A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 117 removed outlier: 4.335A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.649A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.559A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.178A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.014A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.731A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 23 through 30 removed outlier: 7.987A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.860A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.335A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.731A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.559A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.177A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.732A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.632A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1097 1002 hydrogen bonds defined for protein. 2682 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: 6.84 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8147 1.34 - 1.46: 6541 1.46 - 1.59: 11451 1.59 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 26280 Sorted by residual: bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.38e+00 ... (remaining 26275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 34354 1.26 - 2.53: 1144 2.53 - 3.79: 235 3.79 - 5.05: 21 5.05 - 6.31: 12 Bond angle restraints: 35766 Sorted by residual: angle pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" C ASN A 343 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.16e+01 angle pdb=" N ASN B 343 " pdb=" CA ASN B 343 " pdb=" C ASN B 343 " ideal model delta sigma weight residual 111.30 117.61 -6.31 1.36e+00 5.41e-01 2.15e+01 angle pdb=" N ASN C 343 " pdb=" CA ASN C 343 " pdb=" C ASN C 343 " ideal model delta sigma weight residual 111.30 117.58 -6.28 1.36e+00 5.41e-01 2.13e+01 angle pdb=" C ALA A 344 " pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C ALA C 344 " pdb=" N THR C 345 " pdb=" CA THR C 345 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 ... (remaining 35761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14992 17.77 - 35.54: 1112 35.54 - 53.31: 192 53.31 - 71.09: 51 71.09 - 88.86: 27 Dihedral angle restraints: 16374 sinusoidal: 7080 harmonic: 9294 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.64 55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.62 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 16371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3728 0.075 - 0.151: 467 0.151 - 0.226: 11 0.226 - 0.301: 3 0.301 - 0.377: 3 Chirality restraints: 4212 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 4209 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN A 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG A1307 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN C 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.002 2.00e-02 2.50e+03 3.60e-02 1.62e+01 pdb=" CG ASN B 343 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " 0.038 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1545 2.74 - 3.28: 23821 3.28 - 3.82: 38865 3.82 - 4.36: 46837 4.36 - 4.90: 84509 Nonbonded interactions: 195577 Sorted by model distance: nonbonded pdb=" O PRO A 589 " pdb=" OH TYR B 837 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 735 " pdb=" OG1 THR C 859 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B 735 " pdb=" OG1 THR B 859 " model vdw 2.198 3.040 nonbonded pdb=" O PRO B 589 " pdb=" OH TYR C 837 " model vdw 2.201 3.040 ... (remaining 195572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.670 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.003 0.039 26376 Z= 0.157 Angle : 0.584 10.868 36012 Z= 0.287 Chirality : 0.047 0.377 4212 Planarity : 0.004 0.040 4551 Dihedral : 12.909 88.858 10266 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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 aren not related in a simple way. whole: 0.45 (0.15), residues: 3147 helix: 2.44 (0.21), residues: 687 sheet: 1.27 (0.18), residues: 762 loop : -1.16 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.021 0.001 TYR C 904 PHE 0.028 0.001 PHE B 906 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (26280) covalent geometry : angle 0.53704 (35766) SS BOND : bond 0.00311 ( 42) SS BOND : angle 1.11450 ( 84) hydrogen bonds : bond 0.13422 ( 996) hydrogen bonds : angle 5.66490 ( 2682) link_BETA1-4 : bond 0.00316 ( 9) link_BETA1-4 : angle 0.88271 ( 27) link_NAG-ASN : bond 0.00543 ( 45) link_NAG-ASN : angle 3.69256 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 190 average time/residue: 0.7403 time to fit residues: 161.7487 Evaluate side-chains 115 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 745 ASP 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: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0010 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 7.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 965 GLN A1005 GLN B 519 HIS B 965 GLN C 52 GLN C 121 ASN C 519 HIS C 965 GLN C1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.071859 restraints weight = 43745.309| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.02 r_work: 0.2847 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26376 Z= 0.190 Angle : 0.621 10.020 36012 Z= 0.320 Chirality : 0.049 0.376 4212 Planarity : 0.005 0.042 4551 Dihedral : 6.797 58.639 4556 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.76 % Allowed : 5.32 % Favored : 93.92 % 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 aren not related in a simple way. whole: 0.22 (0.15), residues: 3147 helix: 2.05 (0.20), residues: 714 sheet: 1.22 (0.18), residues: 765 loop : -1.31 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1107 TYR 0.031 0.002 TYR B 904 PHE 0.031 0.002 PHE B 906 TRP 0.007 0.001 TRP C 436 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00465 (26280) covalent geometry : angle 0.58978 (35766) SS BOND : bond 0.00305 ( 42) SS BOND : angle 1.55541 ( 84) hydrogen bonds : bond 0.06896 ( 996) hydrogen bonds : angle 5.13721 ( 2682) link_BETA1-4 : bond 0.00271 ( 9) link_BETA1-4 : angle 1.09885 ( 27) link_NAG-ASN : bond 0.00466 ( 45) link_NAG-ASN : angle 2.98764 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.004 Fit side-chains REVERT: B 111 ASP cc_start: 0.7408 (t0) cc_final: 0.6603 (t0) REVERT: B 900 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8701 (mtm) REVERT: C 200 TYR cc_start: 0.8101 (m-80) cc_final: 0.7806 (m-80) REVERT: C 868 GLU cc_start: 0.8474 (mp0) cc_final: 0.8138 (mp0) REVERT: C 869 MET cc_start: 0.9013 (mtt) cc_final: 0.8672 (mtt) outliers start: 21 outliers final: 7 residues processed: 140 average time/residue: 0.7614 time to fit residues: 122.6868 Evaluate side-chains 124 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 153 optimal weight: 0.6980 chunk 268 optimal weight: 0.9980 chunk 237 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073024 restraints weight = 43659.464| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.01 r_work: 0.2856 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26376 Z= 0.133 Angle : 0.564 9.997 36012 Z= 0.289 Chirality : 0.047 0.348 4212 Planarity : 0.004 0.044 4551 Dihedral : 6.359 57.320 4554 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 7.23 % Favored : 91.91 % 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 aren not related in a simple way. whole: 0.31 (0.15), residues: 3147 helix: 2.14 (0.20), residues: 714 sheet: 1.29 (0.18), residues: 765 loop : -1.27 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.019 0.001 TYR C 904 PHE 0.016 0.001 PHE B 906 TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00312 (26280) covalent geometry : angle 0.53198 (35766) SS BOND : bond 0.00246 ( 42) SS BOND : angle 1.27793 ( 84) hydrogen bonds : bond 0.05977 ( 996) hydrogen bonds : angle 4.95401 ( 2682) link_BETA1-4 : bond 0.00288 ( 9) link_BETA1-4 : angle 1.04667 ( 27) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.92613 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.106 Fit side-chains REVERT: B 111 ASP cc_start: 0.7361 (t0) cc_final: 0.6580 (t0) REVERT: B 900 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8642 (mtm) REVERT: C 634 ARG cc_start: 0.6557 (tpt170) cc_final: 0.5781 (tmt-80) REVERT: C 990 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7885 (mp0) outliers start: 24 outliers final: 8 residues processed: 144 average time/residue: 0.7373 time to fit residues: 122.2796 Evaluate side-chains 128 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 10 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.070771 restraints weight = 43380.924| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.99 r_work: 0.2817 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 26376 Z= 0.203 Angle : 0.626 10.183 36012 Z= 0.322 Chirality : 0.049 0.362 4212 Planarity : 0.005 0.047 4551 Dihedral : 6.374 58.936 4554 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.11 % Allowed : 7.77 % Favored : 91.12 % 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 aren not related in a simple way. whole: 0.16 (0.15), residues: 3147 helix: 1.84 (0.20), residues: 729 sheet: 1.24 (0.18), residues: 765 loop : -1.33 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 319 TYR 0.020 0.002 TYR C1067 PHE 0.018 0.002 PHE A 906 TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00505 (26280) covalent geometry : angle 0.59445 (35766) SS BOND : bond 0.00320 ( 42) SS BOND : angle 1.60387 ( 84) hydrogen bonds : bond 0.07190 ( 996) hydrogen bonds : angle 5.10154 ( 2682) link_BETA1-4 : bond 0.00241 ( 9) link_BETA1-4 : angle 1.23156 ( 27) link_NAG-ASN : bond 0.00448 ( 45) link_NAG-ASN : angle 3.00219 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.899 Fit side-chains REVERT: A 111 ASP cc_start: 0.7422 (t0) cc_final: 0.6798 (t0) REVERT: A 990 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 111 ASP cc_start: 0.7408 (t0) cc_final: 0.6915 (t0) REVERT: B 675 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7737 (mp10) REVERT: B 900 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8819 (mtm) REVERT: C 111 ASP cc_start: 0.7375 (t0) cc_final: 0.6770 (t0) REVERT: C 634 ARG cc_start: 0.6582 (tpt170) cc_final: 0.5781 (tmt-80) REVERT: C 990 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7970 (mp0) outliers start: 31 outliers final: 13 residues processed: 152 average time/residue: 0.6567 time to fit residues: 115.5151 Evaluate side-chains 140 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 34 optimal weight: 1.9990 chunk 306 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 191 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.073385 restraints weight = 43334.905| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.02 r_work: 0.2882 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26376 Z= 0.115 Angle : 0.553 10.171 36012 Z= 0.282 Chirality : 0.046 0.342 4212 Planarity : 0.004 0.049 4551 Dihedral : 6.091 58.232 4554 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.93 % Allowed : 8.77 % Favored : 90.29 % 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 aren not related in a simple way. whole: 0.37 (0.15), residues: 3147 helix: 2.16 (0.20), residues: 714 sheet: 1.37 (0.18), residues: 765 loop : -1.24 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 319 TYR 0.016 0.001 TYR C1067 PHE 0.008 0.001 PHE B 238 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00259 (26280) covalent geometry : angle 0.51977 (35766) SS BOND : bond 0.00253 ( 42) SS BOND : angle 1.19580 ( 84) hydrogen bonds : bond 0.05425 ( 996) hydrogen bonds : angle 4.81282 ( 2682) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 0.99842 ( 27) link_NAG-ASN : bond 0.00465 ( 45) link_NAG-ASN : angle 2.96478 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.726 Fit side-chains REVERT: A 111 ASP cc_start: 0.7230 (t0) cc_final: 0.6641 (t0) REVERT: B 111 ASP cc_start: 0.7376 (t0) cc_final: 0.6618 (t0) REVERT: B 586 ASP cc_start: 0.8842 (m-30) cc_final: 0.8616 (m-30) REVERT: B 900 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8766 (mtm) REVERT: C 111 ASP cc_start: 0.7326 (t0) cc_final: 0.6746 (t0) REVERT: C 990 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7814 (mp0) outliers start: 26 outliers final: 12 residues processed: 148 average time/residue: 0.5801 time to fit residues: 99.9481 Evaluate side-chains 135 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 115 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072099 restraints weight = 43683.741| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.02 r_work: 0.2852 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26376 Z= 0.147 Angle : 0.577 9.972 36012 Z= 0.295 Chirality : 0.047 0.345 4212 Planarity : 0.004 0.047 4551 Dihedral : 5.991 57.557 4554 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.19 % Allowed : 9.06 % Favored : 89.75 % 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 aren not related in a simple way. whole: 0.32 (0.15), residues: 3147 helix: 2.09 (0.20), residues: 717 sheet: 1.36 (0.18), residues: 765 loop : -1.28 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 319 TYR 0.019 0.001 TYR C1067 PHE 0.012 0.001 PHE C 898 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00354 (26280) covalent geometry : angle 0.54505 (35766) SS BOND : bond 0.00285 ( 42) SS BOND : angle 1.37282 ( 84) hydrogen bonds : bond 0.06141 ( 996) hydrogen bonds : angle 4.87112 ( 2682) link_BETA1-4 : bond 0.00283 ( 9) link_BETA1-4 : angle 1.10369 ( 27) link_NAG-ASN : bond 0.00443 ( 45) link_NAG-ASN : angle 2.92474 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.081 Fit side-chains REVERT: A 111 ASP cc_start: 0.7388 (t0) cc_final: 0.6800 (t0) REVERT: A 661 GLU cc_start: 0.8301 (mp0) cc_final: 0.8093 (pm20) REVERT: A 1092 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: B 111 ASP cc_start: 0.7386 (t0) cc_final: 0.6647 (t0) REVERT: B 586 ASP cc_start: 0.8857 (m-30) cc_final: 0.8607 (m-30) REVERT: B 1092 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: C 111 ASP cc_start: 0.7335 (t0) cc_final: 0.6756 (t0) REVERT: C 985 ASP cc_start: 0.7990 (t70) cc_final: 0.7774 (t70) REVERT: C 990 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7833 (mp0) outliers start: 33 outliers final: 14 residues processed: 151 average time/residue: 0.6558 time to fit residues: 115.2495 Evaluate side-chains 138 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 301 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 101 optimal weight: 0.0370 chunk 313 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 235 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A1005 GLN B 69 HIS C 69 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074270 restraints weight = 43334.449| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.01 r_work: 0.2887 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26376 Z= 0.108 Angle : 0.542 9.975 36012 Z= 0.275 Chirality : 0.046 0.337 4212 Planarity : 0.004 0.046 4551 Dihedral : 5.720 56.252 4554 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.04 % Allowed : 9.46 % Favored : 89.50 % 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 aren not related in a simple way. whole: 0.45 (0.15), residues: 3147 helix: 2.21 (0.21), residues: 717 sheet: 1.44 (0.18), residues: 765 loop : -1.20 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 319 TYR 0.016 0.001 TYR C1067 PHE 0.007 0.001 PHE A1121 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00239 (26280) covalent geometry : angle 0.51077 (35766) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.12358 ( 84) hydrogen bonds : bond 0.05085 ( 996) hydrogen bonds : angle 4.71412 ( 2682) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 0.97396 ( 27) link_NAG-ASN : bond 0.00477 ( 45) link_NAG-ASN : angle 2.87894 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.860 Fit side-chains REVERT: A 111 ASP cc_start: 0.7214 (t0) cc_final: 0.6641 (t0) REVERT: A 200 TYR cc_start: 0.7834 (m-80) cc_final: 0.7461 (m-80) REVERT: A 215 ASP cc_start: 0.7280 (t0) cc_final: 0.6508 (p0) REVERT: B 53 ASP cc_start: 0.7834 (t70) cc_final: 0.7563 (t70) REVERT: B 111 ASP cc_start: 0.7345 (t0) cc_final: 0.6649 (t0) REVERT: B 466 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8188 (ttp-170) REVERT: B 586 ASP cc_start: 0.8811 (m-30) cc_final: 0.8603 (m-30) REVERT: B 675 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: B 790 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8648 (mtmm) REVERT: C 111 ASP cc_start: 0.7317 (t0) cc_final: 0.6745 (t0) REVERT: C 200 TYR cc_start: 0.7990 (m-80) cc_final: 0.7654 (m-80) outliers start: 29 outliers final: 10 residues processed: 157 average time/residue: 0.5946 time to fit residues: 109.0509 Evaluate side-chains 136 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 50 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 207 optimal weight: 0.0870 chunk 275 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 213 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.071954 restraints weight = 43665.554| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.02 r_work: 0.2851 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26376 Z= 0.155 Angle : 0.583 9.882 36012 Z= 0.299 Chirality : 0.048 0.342 4212 Planarity : 0.004 0.045 4551 Dihedral : 5.803 57.316 4554 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.01 % Allowed : 9.82 % Favored : 89.18 % 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 aren not related in a simple way. whole: 0.37 (0.15), residues: 3147 helix: 2.07 (0.20), residues: 729 sheet: 1.40 (0.18), residues: 765 loop : -1.25 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 319 TYR 0.019 0.001 TYR C1067 PHE 0.012 0.001 PHE C 898 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00376 (26280) covalent geometry : angle 0.55157 (35766) SS BOND : bond 0.00300 ( 42) SS BOND : angle 1.45796 ( 84) hydrogen bonds : bond 0.06187 ( 996) hydrogen bonds : angle 4.84650 ( 2682) link_BETA1-4 : bond 0.00258 ( 9) link_BETA1-4 : angle 1.10754 ( 27) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 2.89383 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.949 Fit side-chains REVERT: A 111 ASP cc_start: 0.7366 (t0) cc_final: 0.6790 (t0) REVERT: A 215 ASP cc_start: 0.7413 (t0) cc_final: 0.6633 (p0) REVERT: A 904 TYR cc_start: 0.8216 (m-10) cc_final: 0.8014 (m-10) REVERT: B 111 ASP cc_start: 0.7363 (t0) cc_final: 0.6660 (t0) REVERT: B 586 ASP cc_start: 0.8853 (m-30) cc_final: 0.8623 (m-30) REVERT: B 1092 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: C 111 ASP cc_start: 0.7345 (t0) cc_final: 0.6767 (t0) REVERT: C 990 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7786 (mp0) outliers start: 28 outliers final: 15 residues processed: 148 average time/residue: 0.6489 time to fit residues: 110.6017 Evaluate side-chains 145 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 129 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 285 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 0.0010 chunk 49 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 210 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.074364 restraints weight = 43451.391| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.02 r_work: 0.2892 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26376 Z= 0.106 Angle : 0.545 9.798 36012 Z= 0.277 Chirality : 0.046 0.333 4212 Planarity : 0.004 0.057 4551 Dihedral : 5.536 56.335 4554 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.79 % Allowed : 10.25 % Favored : 88.96 % 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 aren not related in a simple way. whole: 0.51 (0.15), residues: 3147 helix: 2.26 (0.21), residues: 717 sheet: 1.49 (0.18), residues: 765 loop : -1.17 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 319 TYR 0.016 0.001 TYR A1067 PHE 0.008 0.001 PHE B 133 TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00235 (26280) covalent geometry : angle 0.51488 (35766) SS BOND : bond 0.00283 ( 42) SS BOND : angle 1.10179 ( 84) hydrogen bonds : bond 0.04958 ( 996) hydrogen bonds : angle 4.67114 ( 2682) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 0.98708 ( 27) link_NAG-ASN : bond 0.00482 ( 45) link_NAG-ASN : angle 2.83969 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.767 Fit side-chains REVERT: A 111 ASP cc_start: 0.7080 (t0) cc_final: 0.6463 (t0) REVERT: A 200 TYR cc_start: 0.7821 (m-80) cc_final: 0.7471 (m-80) REVERT: A 215 ASP cc_start: 0.7509 (t0) cc_final: 0.6734 (p0) REVERT: B 53 ASP cc_start: 0.7818 (t70) cc_final: 0.7521 (t70) REVERT: B 111 ASP cc_start: 0.7323 (t0) cc_final: 0.6635 (t0) REVERT: B 661 GLU cc_start: 0.8140 (mp0) cc_final: 0.7848 (mm-30) REVERT: B 790 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8654 (mtmm) REVERT: B 1092 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: C 111 ASP cc_start: 0.7293 (t0) cc_final: 0.6730 (t0) REVERT: C 200 TYR cc_start: 0.7953 (m-80) cc_final: 0.7631 (m-80) REVERT: C 990 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7686 (mp0) outliers start: 22 outliers final: 11 residues processed: 150 average time/residue: 0.6187 time to fit residues: 107.4581 Evaluate side-chains 138 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 24 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 chunk 177 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075093 restraints weight = 43380.507| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.00 r_work: 0.2904 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26376 Z= 0.104 Angle : 0.541 9.763 36012 Z= 0.275 Chirality : 0.046 0.328 4212 Planarity : 0.004 0.054 4551 Dihedral : 5.429 56.431 4554 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.58 % Allowed : 10.79 % Favored : 88.64 % 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 aren not related in a simple way. whole: 0.56 (0.15), residues: 3147 helix: 2.32 (0.21), residues: 717 sheet: 1.52 (0.18), residues: 765 loop : -1.15 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 319 TYR 0.016 0.001 TYR C1067 PHE 0.007 0.001 PHE A 133 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.000 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00227 (26280) covalent geometry : angle 0.51182 (35766) SS BOND : bond 0.00258 ( 42) SS BOND : angle 1.05817 ( 84) hydrogen bonds : bond 0.04749 ( 996) hydrogen bonds : angle 4.61627 ( 2682) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 0.96662 ( 27) link_NAG-ASN : bond 0.00484 ( 45) link_NAG-ASN : angle 2.79620 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6294 Ramachandran restraints generated. 3147 Oldfield, 0 Emsley, 3147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.793 Fit side-chains REVERT: A 111 ASP cc_start: 0.7072 (t0) cc_final: 0.6461 (t0) REVERT: A 200 TYR cc_start: 0.7747 (m-80) cc_final: 0.7383 (m-80) REVERT: A 215 ASP cc_start: 0.7484 (t0) cc_final: 0.6698 (p0) REVERT: B 53 ASP cc_start: 0.7833 (t70) cc_final: 0.7508 (t70) REVERT: B 111 ASP cc_start: 0.7303 (t0) cc_final: 0.6615 (t0) REVERT: B 790 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8662 (mtmm) REVERT: B 1092 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: C 111 ASP cc_start: 0.7275 (t0) cc_final: 0.6709 (t0) REVERT: C 200 TYR cc_start: 0.7929 (m-80) cc_final: 0.7623 (m-80) outliers start: 16 outliers final: 9 residues processed: 145 average time/residue: 0.6585 time to fit residues: 110.0445 Evaluate side-chains 139 residues out of total 2781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 199 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1005 GLN C 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072846 restraints weight = 43214.868| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.99 r_work: 0.2869 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26376 Z= 0.139 Angle : 0.580 9.756 36012 Z= 0.297 Chirality : 0.047 0.334 4212 Planarity : 0.004 0.058 4551 Dihedral : 5.516 57.169 4554 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.76 % Allowed : 10.82 % Favored : 88.42 % 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 aren not related in a simple way. whole: 0.47 (0.15), residues: 3147 helix: 2.25 (0.21), residues: 717 sheet: 1.46 (0.18), residues: 765 loop : -1.21 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 319 TYR 0.019 0.001 TYR C1067 PHE 0.011 0.001 PHE A 898 TRP 0.008 0.001 TRP B 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00332 (26280) covalent geometry : angle 0.55074 (35766) SS BOND : bond 0.00269 ( 42) SS BOND : angle 1.36341 ( 84) hydrogen bonds : bond 0.05836 ( 996) hydrogen bonds : angle 4.76569 ( 2682) link_BETA1-4 : bond 0.00283 ( 9) link_BETA1-4 : angle 1.06501 ( 27) link_NAG-ASN : bond 0.00445 ( 45) link_NAG-ASN : angle 2.81385 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9258.36 seconds wall clock time: 158 minutes 9.09 seconds (9489.09 seconds total)