Starting phenix.real_space_refine on Sun Jun 22 14:28:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgx_32491/06_2025/7wgx_32491.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.108 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 16329 2.51 5 N 4182 2.21 5 O 5001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.46s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25629 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "B" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "C" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1055, 8234 Classifications: {'peptide': 1055} Link IDs: {'PTRANS': 50, 'TRANS': 1004} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 169 Unusual residues: {'BLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.60, per 1000 atoms: 0.61 Number of scatterers: 25629 At special positions: 0 Unit cell: (139.05, 133.65, 179.55, 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 5001 8.00 N 4182 7.00 C 16329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1601 " - " ASN A 343 " " NAG A1602 " - " ASN A 331 " " NAG A1603 " - " ASN A 61 " " NAG A1604 " - " ASN A 616 " " NAG A1605 " - " ASN A1134 " " NAG A1606 " - " ASN A 282 " " NAG A1607 " - " ASN A 709 " " NAG A1608 " - " ASN A 165 " " NAG A1609 " - " ASN A1074 " " NAG B1601 " - " ASN B 343 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 61 " " NAG B1604 " - " ASN B 616 " " NAG B1605 " - " ASN B1134 " " NAG B1606 " - " ASN B 282 " " NAG B1607 " - " ASN B 709 " " NAG B1608 " - " ASN B 165 " " NAG B1609 " - " ASN B1074 " " NAG C1601 " - " ASN C 343 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 61 " " NAG C1604 " - " ASN C 616 " " NAG C1605 " - " ASN C1134 " " NAG C1606 " - " ASN C 282 " " NAG C1607 " - " ASN C 709 " " NAG C1608 " - " ASN C 165 " " NAG C1609 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 122 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 122 " " NAG R 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.93 Conformation dependent library (CDL) restraints added in 3.4 seconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 26.4% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.520A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.322A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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: 3.501A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 855 removed outlier: 4.150A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.637A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.849A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.575A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.913A pdb=" N GLU A 990 " --> pdb=" O LYS A 986 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' 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: 3.520A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.320A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.177A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 removed outlier: 4.149A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.575A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.913A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1140 through 1145' 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: 3.521A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.073A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.322A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.178A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.538A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.502A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 removed outlier: 4.150A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.679A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.745A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.638A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.526A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.848A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (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: 3.575A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.914A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.644A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.019A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.663A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.751A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.771A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.310A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.371A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.455A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.875A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.472A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.018A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.751A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.769A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.310A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.036A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.372A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.456A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.885A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.799A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.019A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.752A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.770A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.036A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.372A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.456A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.473A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.528A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 2829 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: 14.82 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.33: 7146 1.33 - 1.51: 9211 1.51 - 1.69: 9656 1.69 - 1.88: 165 1.88 - 2.06: 9 Bond restraints: 26187 Sorted by residual: bond pdb=" C1A BLR C1610 " pdb=" CHA BLR C1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.79e+02 bond pdb=" C1A BLR A1610 " pdb=" CHA BLR A1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.78e+02 bond pdb=" C1A BLR B1610 " pdb=" CHA BLR B1610 " ideal model delta sigma weight residual 1.498 2.056 -0.558 2.00e-02 2.50e+03 7.77e+02 bond pdb=" C2B BLR C1610 " pdb=" CMB BLR C1610 " ideal model delta sigma weight residual 1.489 1.954 -0.465 2.00e-02 2.50e+03 5.40e+02 bond pdb=" C2B BLR B1610 " pdb=" CMB BLR B1610 " ideal model delta sigma weight residual 1.489 1.954 -0.465 2.00e-02 2.50e+03 5.40e+02 ... (remaining 26182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.38: 35595 9.38 - 18.76: 9 18.76 - 28.13: 3 28.13 - 37.51: 6 37.51 - 46.89: 12 Bond angle restraints: 35625 Sorted by residual: angle pdb=" C2B BLR B1610 " pdb=" C1B BLR B1610 " pdb=" CHB BLR B1610 " ideal model delta sigma weight residual 123.24 170.13 -46.89 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C2B BLR A1610 " pdb=" C1B BLR A1610 " pdb=" CHB BLR A1610 " ideal model delta sigma weight residual 123.24 170.07 -46.83 3.00e+00 1.11e-01 2.44e+02 angle pdb=" C2B BLR C1610 " pdb=" C1B BLR C1610 " pdb=" CHB BLR C1610 " ideal model delta sigma weight residual 123.24 170.06 -46.82 3.00e+00 1.11e-01 2.44e+02 angle pdb=" NB BLR B1610 " pdb=" C1B BLR B1610 " pdb=" CHB BLR B1610 " ideal model delta sigma weight residual 130.12 88.81 41.31 3.00e+00 1.11e-01 1.90e+02 angle pdb=" NB BLR A1610 " pdb=" C1B BLR A1610 " pdb=" CHB BLR A1610 " ideal model delta sigma weight residual 130.12 88.82 41.30 3.00e+00 1.11e-01 1.90e+02 ... (remaining 35620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15013 17.97 - 35.94: 995 35.94 - 53.91: 213 53.91 - 71.89: 54 71.89 - 89.86: 39 Dihedral angle restraints: 16314 sinusoidal: 7107 harmonic: 9207 Sorted by residual: dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.03 74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.03 74.03 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 16311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3320 0.051 - 0.102: 626 0.102 - 0.153: 227 0.153 - 0.205: 15 0.205 - 0.256: 6 Chirality restraints: 4194 Sorted by residual: chirality pdb=" CA LYS A 795 " pdb=" N LYS A 795 " pdb=" C LYS A 795 " pdb=" CB LYS A 795 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS C 795 " pdb=" N LYS C 795 " pdb=" C LYS C 795 " pdb=" CB LYS C 795 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LYS B 795 " pdb=" N LYS B 795 " pdb=" C LYS B 795 " pdb=" CB LYS B 795 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4191 not shown) Planarity restraints: 4575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 620 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.22e+01 pdb=" N PRO C 621 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO C 621 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 621 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 621 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 620 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 621 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 621 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 621 " -0.063 5.00e-02 4.00e+02 ... (remaining 4572 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 5424 2.78 - 3.31: 22971 3.31 - 3.84: 39599 3.84 - 4.37: 45774 4.37 - 4.90: 82618 Nonbonded interactions: 196386 Sorted by model distance: nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 191 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE2 GLU A 191 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 91 " pdb=" OE2 GLU B 191 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.281 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.281 3.040 ... (remaining 196381 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 65.130 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.270 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:4.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.017 0.558 26289 Z= 0.875 Angle : 1.203 46.890 35880 Z= 0.451 Chirality : 0.047 0.256 4194 Planarity : 0.005 0.118 4533 Dihedral : 13.506 89.857 10260 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.95 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3117 helix: 0.96 (0.22), residues: 654 sheet: 0.95 (0.18), residues: 744 loop : -0.91 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.000 HIS B 66 PHE 0.010 0.001 PHE C 133 TYR 0.014 0.001 TYR C1067 ARG 0.001 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 42) link_NAG-ASN : angle 2.40249 ( 126) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 0.52161 ( 45) hydrogen bonds : bond 0.11537 ( 994) hydrogen bonds : angle 6.07389 ( 2829) SS BOND : bond 0.00198 ( 42) SS BOND : angle 0.97612 ( 84) covalent geometry : bond 0.01743 (26187) covalent geometry : angle 1.19728 (35625) Misc. bond : bond 0.09463 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 3.024 Fit side-chains REVERT: A 606 ASN cc_start: 0.8206 (t0) cc_final: 0.7996 (t0) REVERT: B 1029 MET cc_start: 0.8715 (tpp) cc_final: 0.8415 (tpp) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3539 time to fit residues: 98.9788 Evaluate side-chains 110 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 183 optimal weight: 3.9990 chunk 286 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1135 ASN ** C 955 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 = 0.3906 r_free = 0.3906 target = 0.135545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110988 restraints weight = 46240.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112980 restraints weight = 32011.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113787 restraints weight = 22982.557| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26289 Z= 0.137 Angle : 0.556 9.131 35880 Z= 0.280 Chirality : 0.045 0.210 4194 Planarity : 0.005 0.118 4533 Dihedral : 8.151 82.140 4626 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.82 % Favored : 95.80 % Rotamer: Outliers : 0.29 % Allowed : 3.27 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3117 helix: 1.48 (0.21), residues: 672 sheet: 0.88 (0.18), residues: 720 loop : -0.85 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS B 66 PHE 0.011 0.001 PHE B1121 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 42) link_NAG-ASN : angle 2.54039 ( 126) link_BETA1-4 : bond 0.00507 ( 15) link_BETA1-4 : angle 1.00102 ( 45) hydrogen bonds : bond 0.04828 ( 994) hydrogen bonds : angle 4.87200 ( 2829) SS BOND : bond 0.00175 ( 42) SS BOND : angle 0.63224 ( 84) covalent geometry : bond 0.00314 (26187) covalent geometry : angle 0.53478 (35625) Misc. bond : bond 0.00140 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 3.318 Fit side-chains REVERT: A 606 ASN cc_start: 0.8310 (t0) cc_final: 0.8021 (t0) REVERT: C 697 MET cc_start: 0.8237 (ptm) cc_final: 0.7988 (ptp) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.3369 time to fit residues: 70.1233 Evaluate side-chains 110 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 173 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 130 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 960 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103455 restraints weight = 46480.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105637 restraints weight = 30091.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.106042 restraints weight = 21881.620| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26289 Z= 0.264 Angle : 0.657 8.171 35880 Z= 0.338 Chirality : 0.048 0.200 4194 Planarity : 0.006 0.120 4533 Dihedral : 8.158 79.180 4626 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.97 % Favored : 94.64 % Rotamer: Outliers : 0.47 % Allowed : 4.91 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 3117 helix: 1.07 (0.21), residues: 669 sheet: 0.72 (0.18), residues: 726 loop : -1.15 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 886 HIS 0.006 0.001 HIS A1064 PHE 0.022 0.002 PHE B 429 TYR 0.025 0.002 TYR B 904 ARG 0.006 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 42) link_NAG-ASN : angle 2.54388 ( 126) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.20761 ( 45) hydrogen bonds : bond 0.06379 ( 994) hydrogen bonds : angle 5.15448 ( 2829) SS BOND : bond 0.00308 ( 42) SS BOND : angle 0.77577 ( 84) covalent geometry : bond 0.00637 (26187) covalent geometry : angle 0.63869 (35625) Misc. bond : bond 0.00179 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 3.911 Fit side-chains REVERT: A 606 ASN cc_start: 0.8610 (t0) cc_final: 0.8286 (t0) REVERT: B 153 MET cc_start: 0.7538 (mmm) cc_final: 0.7145 (mmm) REVERT: B 569 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.4023 time to fit residues: 88.5070 Evaluate side-chains 108 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain C residue 571 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.129212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102386 restraints weight = 46719.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103953 restraints weight = 32036.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104569 restraints weight = 24058.416| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 26289 Z= 0.264 Angle : 0.645 11.647 35880 Z= 0.331 Chirality : 0.048 0.196 4194 Planarity : 0.005 0.121 4533 Dihedral : 8.018 81.459 4626 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.10 % Favored : 94.51 % Rotamer: Outliers : 0.80 % Allowed : 7.23 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3117 helix: 0.91 (0.20), residues: 675 sheet: 0.57 (0.18), residues: 726 loop : -1.33 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 886 HIS 0.005 0.001 HIS A1064 PHE 0.021 0.002 PHE B 429 TYR 0.019 0.002 TYR A1067 ARG 0.007 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 42) link_NAG-ASN : angle 2.44797 ( 126) link_BETA1-4 : bond 0.00320 ( 15) link_BETA1-4 : angle 1.30529 ( 45) hydrogen bonds : bond 0.06185 ( 994) hydrogen bonds : angle 5.18536 ( 2829) SS BOND : bond 0.00324 ( 42) SS BOND : angle 0.78594 ( 84) covalent geometry : bond 0.00639 (26187) covalent geometry : angle 0.62824 (35625) Misc. bond : bond 0.00115 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 3.048 Fit side-chains REVERT: A 606 ASN cc_start: 0.8640 (t0) cc_final: 0.8396 (t0) REVERT: A 725 GLU cc_start: 0.7313 (pt0) cc_final: 0.7070 (pt0) REVERT: A 933 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8331 (tmtt) REVERT: B 153 MET cc_start: 0.7619 (mmm) cc_final: 0.7342 (mmm) REVERT: B 569 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 957 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7796 (tm-30) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 0.3120 time to fit residues: 70.1104 Evaluate side-chains 118 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 143 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 303 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** C 804 GLN ** 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 = 0.3836 r_free = 0.3836 target = 0.128129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102672 restraints weight = 45022.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104609 restraints weight = 28324.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105105 restraints weight = 20031.452| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 26289 Z= 0.211 Angle : 0.595 9.012 35880 Z= 0.306 Chirality : 0.046 0.200 4194 Planarity : 0.005 0.121 4533 Dihedral : 7.808 81.461 4626 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.23 % Favored : 94.39 % Rotamer: Outliers : 1.13 % Allowed : 8.72 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3117 helix: 1.06 (0.20), residues: 675 sheet: 0.55 (0.18), residues: 726 loop : -1.32 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.016 0.002 PHE B1121 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 42) link_NAG-ASN : angle 2.36433 ( 126) link_BETA1-4 : bond 0.00326 ( 15) link_BETA1-4 : angle 1.29470 ( 45) hydrogen bonds : bond 0.05757 ( 994) hydrogen bonds : angle 5.06147 ( 2829) SS BOND : bond 0.00246 ( 42) SS BOND : angle 0.69974 ( 84) covalent geometry : bond 0.00509 (26187) covalent geometry : angle 0.57740 (35625) Misc. bond : bond 0.00105 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 2.805 Fit side-chains REVERT: A 606 ASN cc_start: 0.8564 (t0) cc_final: 0.8359 (t0) REVERT: B 153 MET cc_start: 0.7603 (mmm) cc_final: 0.7213 (mmm) REVERT: B 569 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8251 (mp) REVERT: C 957 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7890 (tm-30) outliers start: 31 outliers final: 22 residues processed: 135 average time/residue: 0.2921 time to fit residues: 71.9465 Evaluate side-chains 124 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 262 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** 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 = 0.3823 r_free = 0.3823 target = 0.129255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.103341 restraints weight = 46032.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105311 restraints weight = 29371.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105829 restraints weight = 21434.734| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 26289 Z= 0.149 Angle : 0.553 9.366 35880 Z= 0.285 Chirality : 0.045 0.195 4194 Planarity : 0.005 0.121 4533 Dihedral : 7.490 80.626 4626 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.43 % Favored : 95.19 % Rotamer: Outliers : 0.87 % Allowed : 9.60 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3117 helix: 1.31 (0.21), residues: 675 sheet: 0.59 (0.18), residues: 726 loop : -1.22 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.011 0.001 HIS C1083 PHE 0.015 0.001 PHE A1121 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 42) link_NAG-ASN : angle 2.23277 ( 126) link_BETA1-4 : bond 0.00389 ( 15) link_BETA1-4 : angle 1.22245 ( 45) hydrogen bonds : bond 0.05163 ( 994) hydrogen bonds : angle 4.92833 ( 2829) SS BOND : bond 0.00177 ( 42) SS BOND : angle 0.94719 ( 84) covalent geometry : bond 0.00353 (26187) covalent geometry : angle 0.53531 (35625) Misc. bond : bond 0.00083 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 2.678 Fit side-chains REVERT: B 153 MET cc_start: 0.7563 (mmm) cc_final: 0.7172 (mmm) REVERT: B 569 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8419 (mp) REVERT: B 1029 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8450 (ttp) REVERT: C 957 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7836 (tm-30) outliers start: 24 outliers final: 17 residues processed: 127 average time/residue: 0.2969 time to fit residues: 69.0857 Evaluate side-chains 121 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 285 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.104816 restraints weight = 46238.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107377 restraints weight = 30635.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107807 restraints weight = 21309.561| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26289 Z= 0.145 Angle : 0.545 10.647 35880 Z= 0.281 Chirality : 0.045 0.193 4194 Planarity : 0.005 0.120 4533 Dihedral : 7.241 80.200 4626 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.94 % Favored : 94.67 % Rotamer: Outliers : 1.34 % Allowed : 9.78 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3117 helix: 1.48 (0.21), residues: 666 sheet: 0.56 (0.18), residues: 729 loop : -1.15 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE A1121 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 42) link_NAG-ASN : angle 2.20537 ( 126) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.20449 ( 45) hydrogen bonds : bond 0.05004 ( 994) hydrogen bonds : angle 4.84727 ( 2829) SS BOND : bond 0.00208 ( 42) SS BOND : angle 0.66311 ( 84) covalent geometry : bond 0.00342 (26187) covalent geometry : angle 0.52842 (35625) Misc. bond : bond 0.00081 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 3.106 Fit side-chains REVERT: A 606 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7829 (m110) REVERT: B 126 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7684 (p) REVERT: B 153 MET cc_start: 0.7577 (mmm) cc_final: 0.7179 (mmm) REVERT: B 569 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 878 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8788 (mt) REVERT: B 1029 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8426 (ttp) REVERT: C 126 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8289 (p) REVERT: C 878 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8787 (mt) outliers start: 37 outliers final: 26 residues processed: 137 average time/residue: 0.3025 time to fit residues: 75.1518 Evaluate side-chains 137 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 100 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 279 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 264 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.129719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104132 restraints weight = 45943.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.106012 restraints weight = 31180.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106434 restraints weight = 23111.198| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26289 Z= 0.138 Angle : 0.539 10.332 35880 Z= 0.278 Chirality : 0.045 0.191 4194 Planarity : 0.005 0.120 4533 Dihedral : 7.114 79.982 4626 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.56 % Favored : 95.06 % Rotamer: Outliers : 1.34 % Allowed : 10.00 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3117 helix: 1.54 (0.21), residues: 666 sheet: 0.56 (0.18), residues: 729 loop : -1.11 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS A1064 PHE 0.014 0.001 PHE A1121 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 42) link_NAG-ASN : angle 2.17584 ( 126) link_BETA1-4 : bond 0.00373 ( 15) link_BETA1-4 : angle 1.18081 ( 45) hydrogen bonds : bond 0.04912 ( 994) hydrogen bonds : angle 4.81316 ( 2829) SS BOND : bond 0.00185 ( 42) SS BOND : angle 0.71686 ( 84) covalent geometry : bond 0.00325 (26187) covalent geometry : angle 0.52263 (35625) Misc. bond : bond 0.00075 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 2.655 Fit side-chains REVERT: A 938 LEU cc_start: 0.7392 (mt) cc_final: 0.7099 (mt) REVERT: B 126 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 153 MET cc_start: 0.7578 (mmm) cc_final: 0.7205 (mmm) REVERT: B 569 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 878 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (mt) REVERT: B 1029 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8459 (ttp) REVERT: C 126 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8284 (p) REVERT: C 878 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8784 (mt) outliers start: 37 outliers final: 25 residues processed: 138 average time/residue: 0.2908 time to fit residues: 73.1799 Evaluate side-chains 136 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 196 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104082 restraints weight = 44823.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106955 restraints weight = 25635.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.108033 restraints weight = 17236.808| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26289 Z= 0.146 Angle : 0.547 11.492 35880 Z= 0.280 Chirality : 0.045 0.187 4194 Planarity : 0.005 0.119 4533 Dihedral : 6.992 80.123 4626 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.00 % Favored : 94.61 % Rotamer: Outliers : 1.31 % Allowed : 10.43 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3117 helix: 1.58 (0.21), residues: 666 sheet: 0.51 (0.18), residues: 735 loop : -1.08 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 PHE 0.013 0.001 PHE A1121 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 42) link_NAG-ASN : angle 2.17277 ( 126) link_BETA1-4 : bond 0.00371 ( 15) link_BETA1-4 : angle 1.17954 ( 45) hydrogen bonds : bond 0.04948 ( 994) hydrogen bonds : angle 4.80275 ( 2829) SS BOND : bond 0.00201 ( 42) SS BOND : angle 0.67954 ( 84) covalent geometry : bond 0.00346 (26187) covalent geometry : angle 0.53061 (35625) Misc. bond : bond 0.00083 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 2.895 Fit side-chains REVERT: A 938 LEU cc_start: 0.7362 (mt) cc_final: 0.7064 (mt) REVERT: B 126 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7702 (p) REVERT: B 153 MET cc_start: 0.7610 (mmm) cc_final: 0.7274 (mmm) REVERT: B 878 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 933 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8229 (mmpt) REVERT: B 1029 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8468 (ttp) REVERT: C 126 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8273 (p) REVERT: C 878 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8795 (mt) outliers start: 36 outliers final: 27 residues processed: 136 average time/residue: 0.2958 time to fit residues: 72.1833 Evaluate side-chains 139 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 16 optimal weight: 0.0010 chunk 245 optimal weight: 7.9990 chunk 163 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN B 901 GLN C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105081 restraints weight = 44463.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108704 restraints weight = 24434.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111024 restraints weight = 16756.456| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 26289 Z= 0.103 Angle : 0.514 10.769 35880 Z= 0.264 Chirality : 0.044 0.186 4194 Planarity : 0.005 0.118 4533 Dihedral : 6.642 77.646 4626 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.95 % Favored : 95.67 % Rotamer: Outliers : 1.02 % Allowed : 10.76 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3117 helix: 1.97 (0.21), residues: 648 sheet: 0.58 (0.18), residues: 738 loop : -0.96 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS A1064 PHE 0.014 0.001 PHE C 65 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 42) link_NAG-ASN : angle 2.03968 ( 126) link_BETA1-4 : bond 0.00429 ( 15) link_BETA1-4 : angle 1.11240 ( 45) hydrogen bonds : bond 0.04247 ( 994) hydrogen bonds : angle 4.64121 ( 2829) SS BOND : bond 0.00143 ( 42) SS BOND : angle 0.61007 ( 84) covalent geometry : bond 0.00232 (26187) covalent geometry : angle 0.49857 (35625) Misc. bond : bond 0.00055 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 2.953 Fit side-chains REVERT: A 938 LEU cc_start: 0.7335 (mt) cc_final: 0.7018 (mt) REVERT: B 126 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7637 (p) REVERT: B 153 MET cc_start: 0.7604 (mmm) cc_final: 0.7276 (mmm) REVERT: B 569 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8314 (mp) REVERT: B 878 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8778 (mt) REVERT: B 933 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8123 (mmpt) REVERT: C 126 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8224 (p) REVERT: C 824 ASN cc_start: 0.8098 (m-40) cc_final: 0.7846 (m-40) outliers start: 28 outliers final: 18 residues processed: 141 average time/residue: 0.2876 time to fit residues: 73.7522 Evaluate side-chains 133 residues out of total 2751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 256 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 270 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN C 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103953 restraints weight = 46407.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105483 restraints weight = 33560.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105930 restraints weight = 25667.822| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26289 Z= 0.210 Angle : 0.591 10.743 35880 Z= 0.303 Chirality : 0.046 0.182 4194 Planarity : 0.005 0.119 4533 Dihedral : 6.971 81.291 4626 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.23 % Favored : 94.39 % Rotamer: Outliers : 1.05 % Allowed : 10.87 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3117 helix: 1.52 (0.21), residues: 666 sheet: 0.48 (0.18), residues: 735 loop : -1.08 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A1064 PHE 0.017 0.002 PHE C 65 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 42) link_NAG-ASN : angle 2.22041 ( 126) link_BETA1-4 : bond 0.00317 ( 15) link_BETA1-4 : angle 1.20459 ( 45) hydrogen bonds : bond 0.05412 ( 994) hydrogen bonds : angle 4.87179 ( 2829) SS BOND : bond 0.00255 ( 42) SS BOND : angle 1.04734 ( 84) covalent geometry : bond 0.00504 (26187) covalent geometry : angle 0.57391 (35625) Misc. bond : bond 0.00083 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6242.08 seconds wall clock time: 111 minutes 1.78 seconds (6661.78 seconds total)