Starting phenix.real_space_refine on Mon Aug 25 07:52:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uul_42589/08_2025/8uul_42589.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 117 5.16 5 C 16496 2.51 5 N 4270 2.21 5 O 5008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s 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: 25891 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8460 Classifications: {'peptide': 1083} Link IDs: {'PTRANS': 57, 'TRANS': 1025} Chain breaks: 5 Chain: "B" Number of atoms: 8474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8474 Classifications: {'peptide': 1084} Link IDs: {'PTRANS': 57, 'TRANS': 1026} Chain breaks: 5 Chain: "C" Number of atoms: 8495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8495 Classifications: {'peptide': 1087} Link IDs: {'PTRANS': 58, 'TRANS': 1028} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.81, per 1000 atoms: 0.22 Number of scatterers: 25891 At special positions: 0 Unit cell: (146.08, 154.933, 177.067, 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 117 16.00 O 5008 8.00 N 4270 7.00 C 16496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, 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-ASN " NAG A1303 " - " ASN A 709 " " NAG B1303 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1302 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 840.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6094 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 46 sheets defined 25.2% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.596A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.554A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.207A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.790A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.740A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.622A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.783A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.512A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.688A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.257A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.135A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.249A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.513A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.868A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.015A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.953A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.606A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.987A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.918A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.529A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.665A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 4.014A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.157A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.645A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.580A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.539A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 635 through 639 removed outlier: 3.911A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 635 through 639' Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.582A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.599A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.882A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.532A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.676A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.560A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.224A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.026A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.195A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.855A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.076A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.562A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 11.033A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.852A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.251A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.234A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.988A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.335A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.917A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.883A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.053A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.533A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 154 through 158 removed outlier: 6.408A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.580A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.793A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.348A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.940A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.941A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.944A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.571A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.155A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.897A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.988A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 13.724A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.643A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 11.676A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.867A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.343A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.244A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.461A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.578A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 6.917A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 1003 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8264 1.34 - 1.47: 6891 1.47 - 1.60: 11185 1.60 - 1.73: 2 1.73 - 1.86: 145 Bond restraints: 26487 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CB THR C 108 " pdb=" OG1 THR C 108 " ideal model delta sigma weight residual 1.433 1.485 -0.052 1.60e-02 3.91e+03 1.06e+01 bond pdb=" CG LEU A 916 " pdb=" CD1 LEU A 916 " ideal model delta sigma weight residual 1.521 1.417 0.104 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CA THR C 108 " pdb=" CB THR C 108 " ideal model delta sigma weight residual 1.528 1.577 -0.048 1.59e-02 3.96e+03 9.27e+00 bond pdb=" CG LEU C 916 " pdb=" CD1 LEU C 916 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.63e+00 ... (remaining 26482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 35247 2.94 - 5.88: 720 5.88 - 8.82: 77 8.82 - 11.76: 12 11.76 - 14.70: 1 Bond angle restraints: 36057 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.76 -7.06 1.22e+00 6.72e-01 3.35e+01 angle pdb=" C LEU B 984 " pdb=" N ASP B 985 " pdb=" CA ASP B 985 " ideal model delta sigma weight residual 120.68 128.91 -8.23 1.52e+00 4.33e-01 2.93e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 117.19 -6.49 1.22e+00 6.72e-01 2.83e+01 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 121.65 116.36 5.29 1.01e+00 9.80e-01 2.74e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 107.73 114.66 -6.93 1.34e+00 5.57e-01 2.67e+01 ... (remaining 36052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15175 21.50 - 42.99: 866 42.99 - 64.49: 130 64.49 - 85.99: 33 85.99 - 107.48: 32 Dihedral angle restraints: 16236 sinusoidal: 6765 harmonic: 9471 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 14.20 78.80 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 171.21 -78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 16233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 4134 0.207 - 0.414: 25 0.414 - 0.621: 1 0.621 - 0.828: 1 0.828 - 1.034: 1 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CB THR C 108 " pdb=" CA THR C 108 " pdb=" OG1 THR C 108 " pdb=" CG2 THR C 108 " both_signs ideal model delta sigma weight residual False 2.55 1.75 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 4159 not shown) Planarity restraints: 4648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.057 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 25 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.032 2.00e-02 2.50e+03 3.08e-02 1.19e+01 pdb=" CG ASN A1098 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 906 " 0.021 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A 906 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 906 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 906 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 906 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 906 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4645 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5717 2.78 - 3.31: 22321 3.31 - 3.84: 41023 3.84 - 4.37: 45893 4.37 - 4.90: 82082 Nonbonded interactions: 197036 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" OD2 ASP C 53 " model vdw 2.259 3.040 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.278 3.040 ... (remaining 197031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 623 or resid 634 through 1306)) selection = (chain 'C' and (resid 14 through 623 or resid 634 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 3.250 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.710 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.009 0.139 26547 Z= 0.409 Angle : 1.057 19.018 36193 Z= 0.582 Chirality : 0.066 1.034 4162 Planarity : 0.007 0.088 4637 Dihedral : 14.634 107.484 10019 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.10 % 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: -1.96 (0.13), residues: 3218 helix: -0.75 (0.18), residues: 670 sheet: -0.09 (0.19), residues: 716 loop : -2.10 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 346 TYR 0.031 0.003 TYR A 904 PHE 0.055 0.003 PHE A 906 TRP 0.029 0.003 TRP B 633 HIS 0.009 0.002 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00929 (26487) covalent geometry : angle 1.03552 (36057) SS BOND : bond 0.00592 ( 41) SS BOND : angle 2.33085 ( 82) hydrogen bonds : bond 0.15108 ( 999) hydrogen bonds : angle 7.16885 ( 2712) Misc. bond : bond 0.00345 ( 1) link_BETA1-4 : bond 0.01083 ( 7) link_BETA1-4 : angle 2.57046 ( 21) link_NAG-ASN : bond 0.01050 ( 11) link_NAG-ASN : angle 6.08978 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4830 (ptp) cc_final: 0.4605 (ptp) REVERT: A 801 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8863 (t0) REVERT: B 168 PHE cc_start: 0.6772 (t80) cc_final: 0.6505 (t80) REVERT: B 177 MET cc_start: 0.5763 (pmm) cc_final: 0.5529 (pmm) REVERT: B 902 MET cc_start: 0.9207 (tpt) cc_final: 0.8875 (tpt) REVERT: C 177 MET cc_start: 0.5509 (pmm) cc_final: 0.5134 (pmm) REVERT: C 197 ILE cc_start: 0.7923 (mp) cc_final: 0.7608 (tp) REVERT: C 380 TYR cc_start: 0.8487 (m-10) cc_final: 0.8144 (m-10) REVERT: C 418 ILE cc_start: 0.9242 (pt) cc_final: 0.8882 (mm) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1581 time to fit residues: 20.8043 Evaluate side-chains 60 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 414 GLN A 519 HIS A 965 GLN B 69 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.079867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051851 restraints weight = 89862.930| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.36 r_work: 0.2870 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26547 Z= 0.132 Angle : 0.615 16.015 36193 Z= 0.315 Chirality : 0.046 0.658 4162 Planarity : 0.004 0.067 4637 Dihedral : 9.443 77.230 4180 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.13 (0.14), residues: 3218 helix: 1.01 (0.20), residues: 673 sheet: 0.15 (0.19), residues: 701 loop : -1.90 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 214 TYR 0.018 0.001 TYR A1067 PHE 0.028 0.001 PHE C 168 TRP 0.011 0.001 TRP C 633 HIS 0.007 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00286 (26487) covalent geometry : angle 0.59576 (36057) SS BOND : bond 0.00317 ( 41) SS BOND : angle 1.46206 ( 82) hydrogen bonds : bond 0.05619 ( 999) hydrogen bonds : angle 5.54440 ( 2712) Misc. bond : bond 0.00122 ( 1) link_BETA1-4 : bond 0.00370 ( 7) link_BETA1-4 : angle 1.61938 ( 21) link_NAG-ASN : bond 0.00557 ( 11) link_NAG-ASN : angle 4.52615 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8661 (pmm) cc_final: 0.8452 (mpp) REVERT: A 200 TYR cc_start: 0.7842 (m-80) cc_final: 0.7464 (m-10) REVERT: A 801 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8623 (t0) REVERT: B 380 TYR cc_start: 0.8803 (m-10) cc_final: 0.8592 (m-10) REVERT: C 177 MET cc_start: 0.5759 (pmm) cc_final: 0.5333 (pmm) REVERT: C 197 ILE cc_start: 0.7931 (mp) cc_final: 0.7541 (tp) REVERT: C 380 TYR cc_start: 0.8664 (m-10) cc_final: 0.8459 (m-10) REVERT: C 786 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8448 (mmmt) outliers start: 2 outliers final: 1 residues processed: 74 average time/residue: 0.1493 time to fit residues: 17.8641 Evaluate side-chains 61 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain C residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 150 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 926 GLN A 957 GLN A1011 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 926 GLN C 919 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049253 restraints weight = 91493.700| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.30 r_work: 0.2784 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 26547 Z= 0.339 Angle : 0.727 16.051 36193 Z= 0.368 Chirality : 0.049 0.672 4162 Planarity : 0.004 0.060 4637 Dihedral : 8.030 78.311 4180 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.63 % Allowed : 6.85 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.19 (0.14), residues: 3218 helix: 1.19 (0.20), residues: 684 sheet: -0.23 (0.19), residues: 732 loop : -1.92 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 214 TYR 0.024 0.002 TYR C1067 PHE 0.025 0.002 PHE A 92 TRP 0.010 0.001 TRP C 64 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00789 (26487) covalent geometry : angle 0.71027 (36057) SS BOND : bond 0.00385 ( 41) SS BOND : angle 1.56361 ( 82) hydrogen bonds : bond 0.06634 ( 999) hydrogen bonds : angle 5.58241 ( 2712) Misc. bond : bond 0.00084 ( 1) link_BETA1-4 : bond 0.00373 ( 7) link_BETA1-4 : angle 1.69744 ( 21) link_NAG-ASN : bond 0.00681 ( 11) link_NAG-ASN : angle 4.49190 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5192 (ptp) cc_final: 0.4738 (ptp) REVERT: A 197 ILE cc_start: 0.7564 (mp) cc_final: 0.6854 (tp) REVERT: A 200 TYR cc_start: 0.7898 (m-80) cc_final: 0.7492 (m-10) REVERT: A 801 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8779 (t0) REVERT: B 197 ILE cc_start: 0.7930 (mp) cc_final: 0.7541 (tp) REVERT: C 177 MET cc_start: 0.5917 (pmm) cc_final: 0.5484 (pmm) REVERT: C 201 PHE cc_start: 0.6891 (t80) cc_final: 0.6294 (t80) REVERT: C 315 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 380 TYR cc_start: 0.8687 (m-10) cc_final: 0.8481 (m-10) REVERT: C 1066 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8845 (p) outliers start: 18 outliers final: 9 residues processed: 79 average time/residue: 0.1321 time to fit residues: 18.2613 Evaluate side-chains 69 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 242 optimal weight: 0.0270 chunk 288 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 926 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.079938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052604 restraints weight = 89617.241| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.31 r_work: 0.2875 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26547 Z= 0.107 Angle : 0.559 15.081 36193 Z= 0.280 Chirality : 0.045 0.632 4162 Planarity : 0.004 0.053 4637 Dihedral : 6.549 64.650 4180 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.53 % Allowed : 8.05 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.70 (0.14), residues: 3218 helix: 1.94 (0.21), residues: 670 sheet: 0.05 (0.19), residues: 714 loop : -1.69 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 214 TYR 0.018 0.001 TYR A 265 PHE 0.016 0.001 PHE B 201 TRP 0.009 0.001 TRP C 633 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00226 (26487) covalent geometry : angle 0.54176 (36057) SS BOND : bond 0.00289 ( 41) SS BOND : angle 1.19171 ( 82) hydrogen bonds : bond 0.04672 ( 999) hydrogen bonds : angle 5.00553 ( 2712) Misc. bond : bond 0.00151 ( 1) link_BETA1-4 : bond 0.00844 ( 7) link_BETA1-4 : angle 1.89572 ( 21) link_NAG-ASN : bond 0.00509 ( 11) link_NAG-ASN : angle 4.06616 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5184 (ptp) cc_final: 0.4755 (ptp) REVERT: A 197 ILE cc_start: 0.7648 (mp) cc_final: 0.6992 (tp) REVERT: A 200 TYR cc_start: 0.7818 (m-80) cc_final: 0.7376 (m-10) REVERT: A 950 ASP cc_start: 0.8706 (t70) cc_final: 0.8264 (t0) REVERT: B 197 ILE cc_start: 0.8044 (mp) cc_final: 0.7688 (tp) REVERT: B 950 ASP cc_start: 0.8750 (t70) cc_final: 0.8403 (t0) REVERT: C 177 MET cc_start: 0.5838 (pmm) cc_final: 0.5464 (pmm) REVERT: C 197 ILE cc_start: 0.8029 (mp) cc_final: 0.7681 (tp) REVERT: C 786 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8385 (mmmt) REVERT: C 1066 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8756 (p) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.1413 time to fit residues: 20.9105 Evaluate side-chains 72 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 70 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 123 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 926 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.077821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050661 restraints weight = 90904.751| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.09 r_work: 0.2848 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 26547 Z= 0.272 Angle : 0.645 15.505 36193 Z= 0.325 Chirality : 0.047 0.636 4162 Planarity : 0.004 0.051 4637 Dihedral : 6.470 65.743 4178 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.74 % Allowed : 9.59 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.83 (0.14), residues: 3218 helix: 1.77 (0.20), residues: 683 sheet: -0.12 (0.19), residues: 729 loop : -1.75 (0.13), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.021 0.002 TYR C1067 PHE 0.019 0.002 PHE B 92 TRP 0.009 0.001 TRP C 64 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00637 (26487) covalent geometry : angle 0.62912 (36057) SS BOND : bond 0.00352 ( 41) SS BOND : angle 1.38304 ( 82) hydrogen bonds : bond 0.05877 ( 999) hydrogen bonds : angle 5.22282 ( 2712) Misc. bond : bond 0.00127 ( 1) link_BETA1-4 : bond 0.00493 ( 7) link_BETA1-4 : angle 1.71848 ( 21) link_NAG-ASN : bond 0.00540 ( 11) link_NAG-ASN : angle 4.22779 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7674 (mp) cc_final: 0.7019 (tp) REVERT: A 200 TYR cc_start: 0.7841 (m-80) cc_final: 0.7413 (m-10) REVERT: A 636 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6586 (t80) REVERT: A 801 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8585 (t0) REVERT: A 950 ASP cc_start: 0.8797 (t70) cc_final: 0.8415 (t0) REVERT: B 197 ILE cc_start: 0.8035 (mp) cc_final: 0.7688 (tp) REVERT: B 902 MET cc_start: 0.9288 (mmm) cc_final: 0.8990 (tpt) REVERT: B 950 ASP cc_start: 0.8865 (t70) cc_final: 0.8520 (t0) REVERT: C 141 LEU cc_start: 0.8421 (mm) cc_final: 0.7451 (tt) REVERT: C 177 MET cc_start: 0.5839 (pmm) cc_final: 0.5469 (pmm) REVERT: C 197 ILE cc_start: 0.7944 (mp) cc_final: 0.7510 (tp) REVERT: C 201 PHE cc_start: 0.6913 (t80) cc_final: 0.6359 (t80) REVERT: C 380 TYR cc_start: 0.8680 (m-10) cc_final: 0.8230 (m-10) REVERT: C 786 LYS cc_start: 0.8799 (mmtm) cc_final: 0.8462 (mmmt) REVERT: C 1066 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8833 (p) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 0.1499 time to fit residues: 22.3499 Evaluate side-chains 73 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 69 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 chunk 165 optimal weight: 0.4980 chunk 243 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052181 restraints weight = 89983.745| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.33 r_work: 0.2866 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26547 Z= 0.104 Angle : 0.544 14.746 36193 Z= 0.273 Chirality : 0.044 0.623 4162 Planarity : 0.003 0.047 4637 Dihedral : 5.840 55.131 4178 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.63 % Allowed : 10.01 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.52 (0.15), residues: 3218 helix: 2.19 (0.21), residues: 673 sheet: 0.06 (0.19), residues: 731 loop : -1.59 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.018 0.001 TYR A1067 PHE 0.023 0.001 PHE B 201 TRP 0.008 0.001 TRP B 104 HIS 0.005 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00224 (26487) covalent geometry : angle 0.52724 (36057) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.11657 ( 82) hydrogen bonds : bond 0.04649 ( 999) hydrogen bonds : angle 4.86500 ( 2712) Misc. bond : bond 0.00162 ( 1) link_BETA1-4 : bond 0.00535 ( 7) link_BETA1-4 : angle 1.67375 ( 21) link_NAG-ASN : bond 0.00482 ( 11) link_NAG-ASN : angle 3.96026 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5363 (ptp) cc_final: 0.5162 (ptp) REVERT: A 197 ILE cc_start: 0.7665 (mp) cc_final: 0.7041 (tp) REVERT: A 200 TYR cc_start: 0.7766 (m-80) cc_final: 0.7341 (m-10) REVERT: A 636 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6419 (t80) REVERT: A 950 ASP cc_start: 0.8705 (t70) cc_final: 0.8315 (t0) REVERT: B 197 ILE cc_start: 0.8030 (mp) cc_final: 0.7697 (tp) REVERT: B 380 TYR cc_start: 0.8801 (m-10) cc_final: 0.8415 (m-10) REVERT: B 950 ASP cc_start: 0.8812 (t70) cc_final: 0.8483 (t0) REVERT: C 141 LEU cc_start: 0.8466 (mm) cc_final: 0.7525 (tt) REVERT: C 177 MET cc_start: 0.5854 (pmm) cc_final: 0.5420 (pmm) REVERT: C 197 ILE cc_start: 0.8061 (mp) cc_final: 0.7711 (tp) REVERT: C 725 GLU cc_start: 0.8853 (tt0) cc_final: 0.8599 (tt0) REVERT: C 786 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8422 (mmmt) REVERT: C 1066 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8790 (p) outliers start: 18 outliers final: 11 residues processed: 91 average time/residue: 0.1678 time to fit residues: 26.4388 Evaluate side-chains 81 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 113 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 57 optimal weight: 0.0370 chunk 70 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.077286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049905 restraints weight = 90807.172| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.12 r_work: 0.2825 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 26547 Z= 0.303 Angle : 0.664 15.566 36193 Z= 0.334 Chirality : 0.047 0.627 4162 Planarity : 0.004 0.048 4637 Dihedral : 6.040 59.496 4178 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.77 % Allowed : 10.54 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.80 (0.14), residues: 3218 helix: 1.78 (0.20), residues: 690 sheet: -0.13 (0.18), residues: 742 loop : -1.73 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.024 0.002 TYR A 279 PHE 0.024 0.002 PHE C 135 TRP 0.011 0.001 TRP C 64 HIS 0.006 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00710 (26487) covalent geometry : angle 0.64805 (36057) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.40596 ( 82) hydrogen bonds : bond 0.06004 ( 999) hydrogen bonds : angle 5.21468 ( 2712) Misc. bond : bond 0.00143 ( 1) link_BETA1-4 : bond 0.00329 ( 7) link_BETA1-4 : angle 1.46103 ( 21) link_NAG-ASN : bond 0.00562 ( 11) link_NAG-ASN : angle 4.21002 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8331 (mt) cc_final: 0.8109 (tp) REVERT: A 177 MET cc_start: 0.5316 (ptp) cc_final: 0.4835 (ptp) REVERT: A 197 ILE cc_start: 0.7669 (mp) cc_final: 0.7007 (tp) REVERT: A 200 TYR cc_start: 0.7918 (m-80) cc_final: 0.7462 (m-10) REVERT: A 636 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6661 (t80) REVERT: A 950 ASP cc_start: 0.8801 (t70) cc_final: 0.8422 (t0) REVERT: B 197 ILE cc_start: 0.8102 (mp) cc_final: 0.7755 (tp) REVERT: B 950 ASP cc_start: 0.8897 (t70) cc_final: 0.8571 (t0) REVERT: C 141 LEU cc_start: 0.8447 (mm) cc_final: 0.7429 (tt) REVERT: C 177 MET cc_start: 0.5888 (pmm) cc_final: 0.5434 (pmm) REVERT: C 197 ILE cc_start: 0.7917 (mp) cc_final: 0.7497 (tp) REVERT: C 380 TYR cc_start: 0.8615 (m-10) cc_final: 0.8281 (m-10) REVERT: C 786 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8481 (mmmt) REVERT: C 1066 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8845 (p) outliers start: 22 outliers final: 13 residues processed: 85 average time/residue: 0.1672 time to fit residues: 24.7122 Evaluate side-chains 77 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 56 optimal weight: 0.0970 chunk 186 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 278 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 281 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.079518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052603 restraints weight = 89852.655| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.15 r_work: 0.2882 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26547 Z= 0.107 Angle : 0.540 14.697 36193 Z= 0.273 Chirality : 0.044 0.625 4162 Planarity : 0.003 0.044 4637 Dihedral : 5.518 55.639 4178 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.60 % Allowed : 10.61 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.46 (0.15), residues: 3218 helix: 2.19 (0.21), residues: 683 sheet: 0.07 (0.19), residues: 739 loop : -1.55 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.018 0.001 TYR C1067 PHE 0.023 0.001 PHE B 201 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00234 (26487) covalent geometry : angle 0.52362 (36057) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.14293 ( 82) hydrogen bonds : bond 0.04723 ( 999) hydrogen bonds : angle 4.83158 ( 2712) Misc. bond : bond 0.00162 ( 1) link_BETA1-4 : bond 0.00458 ( 7) link_BETA1-4 : angle 1.45644 ( 21) link_NAG-ASN : bond 0.00446 ( 11) link_NAG-ASN : angle 3.89961 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8324 (mt) cc_final: 0.8101 (tt) REVERT: A 197 ILE cc_start: 0.7686 (mp) cc_final: 0.7077 (tp) REVERT: A 200 TYR cc_start: 0.7777 (m-80) cc_final: 0.7387 (m-10) REVERT: A 531 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (t) REVERT: A 636 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6457 (t80) REVERT: A 950 ASP cc_start: 0.8693 (t70) cc_final: 0.8319 (t0) REVERT: B 197 ILE cc_start: 0.8104 (mp) cc_final: 0.7761 (tp) REVERT: B 380 TYR cc_start: 0.8727 (m-10) cc_final: 0.8364 (m-10) REVERT: B 950 ASP cc_start: 0.8790 (t70) cc_final: 0.8446 (t0) REVERT: C 141 LEU cc_start: 0.8462 (mm) cc_final: 0.7480 (tt) REVERT: C 177 MET cc_start: 0.5835 (pmm) cc_final: 0.5377 (pmm) REVERT: C 197 ILE cc_start: 0.7979 (mp) cc_final: 0.7637 (tp) REVERT: C 380 TYR cc_start: 0.8571 (m-10) cc_final: 0.8308 (m-10) REVERT: C 725 GLU cc_start: 0.8830 (tt0) cc_final: 0.8579 (tt0) REVERT: C 786 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8414 (mmmt) REVERT: C 1066 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8740 (p) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.1759 time to fit residues: 25.0230 Evaluate side-chains 81 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 122 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 230 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 320 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.078540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051574 restraints weight = 90366.815| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.10 r_work: 0.2863 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26547 Z= 0.166 Angle : 0.558 14.926 36193 Z= 0.281 Chirality : 0.045 0.619 4162 Planarity : 0.003 0.044 4637 Dihedral : 5.400 57.593 4178 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.67 % Allowed : 10.68 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 3218 helix: 2.18 (0.21), residues: 684 sheet: -0.01 (0.18), residues: 753 loop : -1.53 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 646 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE C 135 TRP 0.007 0.001 TRP C 633 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00387 (26487) covalent geometry : angle 0.54227 (36057) SS BOND : bond 0.00288 ( 41) SS BOND : angle 1.16852 ( 82) hydrogen bonds : bond 0.04991 ( 999) hydrogen bonds : angle 4.86497 ( 2712) Misc. bond : bond 0.00149 ( 1) link_BETA1-4 : bond 0.00303 ( 7) link_BETA1-4 : angle 1.33143 ( 21) link_NAG-ASN : bond 0.00429 ( 11) link_NAG-ASN : angle 3.93962 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8383 (mt) cc_final: 0.8150 (tt) REVERT: A 197 ILE cc_start: 0.7721 (mp) cc_final: 0.7110 (tp) REVERT: A 200 TYR cc_start: 0.7825 (m-80) cc_final: 0.7404 (m-10) REVERT: A 380 TYR cc_start: 0.8793 (m-10) cc_final: 0.8466 (m-10) REVERT: A 531 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (t) REVERT: A 636 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.6574 (t80) REVERT: A 902 MET cc_start: 0.9258 (tpp) cc_final: 0.9039 (tpt) REVERT: A 950 ASP cc_start: 0.8734 (t70) cc_final: 0.8363 (t0) REVERT: B 197 ILE cc_start: 0.8122 (mp) cc_final: 0.7784 (tp) REVERT: B 380 TYR cc_start: 0.8712 (m-10) cc_final: 0.8394 (m-10) REVERT: B 902 MET cc_start: 0.9329 (mmm) cc_final: 0.9066 (tpt) REVERT: B 950 ASP cc_start: 0.8834 (t70) cc_final: 0.8502 (t0) REVERT: C 52 GLN cc_start: 0.9257 (tt0) cc_final: 0.8771 (tp-100) REVERT: C 141 LEU cc_start: 0.8493 (mm) cc_final: 0.7467 (tt) REVERT: C 177 MET cc_start: 0.5788 (pmm) cc_final: 0.5311 (pmm) REVERT: C 197 ILE cc_start: 0.7993 (mp) cc_final: 0.7634 (tp) REVERT: C 380 TYR cc_start: 0.8578 (m-10) cc_final: 0.8327 (m-10) REVERT: C 725 GLU cc_start: 0.8842 (tt0) cc_final: 0.8605 (tt0) REVERT: C 786 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8422 (mmmt) REVERT: C 1066 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8781 (p) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.1668 time to fit residues: 25.2735 Evaluate side-chains 86 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 83 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 27 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 255 optimal weight: 50.0000 chunk 254 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.079780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052933 restraints weight = 89793.978| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 4.14 r_work: 0.2893 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26547 Z= 0.124 Angle : 0.539 16.888 36193 Z= 0.269 Chirality : 0.044 0.615 4162 Planarity : 0.003 0.043 4637 Dihedral : 5.134 56.144 4178 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.67 % Allowed : 10.75 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.36 (0.15), residues: 3218 helix: 2.26 (0.21), residues: 685 sheet: 0.11 (0.19), residues: 737 loop : -1.47 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 646 TYR 0.018 0.001 TYR C1067 PHE 0.022 0.001 PHE B 201 TRP 0.008 0.001 TRP C 633 HIS 0.005 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00285 (26487) covalent geometry : angle 0.52418 (36057) SS BOND : bond 0.00262 ( 41) SS BOND : angle 1.08972 ( 82) hydrogen bonds : bond 0.04572 ( 999) hydrogen bonds : angle 4.73043 ( 2712) Misc. bond : bond 0.00147 ( 1) link_BETA1-4 : bond 0.00417 ( 7) link_BETA1-4 : angle 1.32489 ( 21) link_NAG-ASN : bond 0.00435 ( 11) link_NAG-ASN : angle 3.81335 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8371 (mt) cc_final: 0.8140 (tt) REVERT: A 177 MET cc_start: 0.5646 (ptp) cc_final: 0.5253 (ptp) REVERT: A 197 ILE cc_start: 0.7741 (mp) cc_final: 0.7151 (tp) REVERT: A 200 TYR cc_start: 0.7754 (m-80) cc_final: 0.7388 (m-10) REVERT: A 380 TYR cc_start: 0.8788 (m-10) cc_final: 0.8483 (m-10) REVERT: A 636 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.6629 (t80) REVERT: A 725 GLU cc_start: 0.8871 (tt0) cc_final: 0.8670 (tt0) REVERT: A 950 ASP cc_start: 0.8710 (t70) cc_final: 0.8333 (t0) REVERT: B 197 ILE cc_start: 0.8150 (mp) cc_final: 0.7818 (tp) REVERT: B 380 TYR cc_start: 0.8741 (m-10) cc_final: 0.8458 (m-10) REVERT: B 950 ASP cc_start: 0.8804 (t70) cc_final: 0.8453 (t0) REVERT: B 988 GLU cc_start: 0.9176 (mp0) cc_final: 0.8927 (mp0) REVERT: C 52 GLN cc_start: 0.9260 (tt0) cc_final: 0.8777 (tp-100) REVERT: C 141 LEU cc_start: 0.8469 (mm) cc_final: 0.7401 (tt) REVERT: C 177 MET cc_start: 0.5705 (pmm) cc_final: 0.5321 (pmm) REVERT: C 197 ILE cc_start: 0.7995 (mp) cc_final: 0.7650 (tp) REVERT: C 380 TYR cc_start: 0.8559 (m-10) cc_final: 0.8331 (m-10) REVERT: C 725 GLU cc_start: 0.8852 (tt0) cc_final: 0.8613 (tt0) REVERT: C 786 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8440 (mmmt) REVERT: C 1066 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8769 (p) outliers start: 19 outliers final: 14 residues processed: 97 average time/residue: 0.1628 time to fit residues: 27.1172 Evaluate side-chains 88 residues out of total 2846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 40 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 291 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 804 GLN A 926 GLN ** A1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B 331 ASN C 437 ASN C 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.075509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048296 restraints weight = 91269.305| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.14 r_work: 0.2780 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 26547 Z= 0.451 Angle : 0.819 16.068 36193 Z= 0.411 Chirality : 0.051 0.633 4162 Planarity : 0.004 0.046 4637 Dihedral : 6.139 58.979 4178 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.70 % Allowed : 11.17 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.12 (0.14), residues: 3218 helix: 1.36 (0.20), residues: 693 sheet: -0.28 (0.18), residues: 762 loop : -1.91 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 646 TYR 0.033 0.002 TYR A 279 PHE 0.027 0.002 PHE A 92 TRP 0.019 0.002 TRP A 104 HIS 0.008 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.01049 (26487) covalent geometry : angle 0.80477 (36057) SS BOND : bond 0.00543 ( 41) SS BOND : angle 1.70937 ( 82) hydrogen bonds : bond 0.07158 ( 999) hydrogen bonds : angle 5.59915 ( 2712) Misc. bond : bond 0.00165 ( 1) link_BETA1-4 : bond 0.00545 ( 7) link_BETA1-4 : angle 1.48583 ( 21) link_NAG-ASN : bond 0.00861 ( 11) link_NAG-ASN : angle 4.41483 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.53 seconds wall clock time: 100 minutes 20.87 seconds (6020.87 seconds total)