Starting phenix.real_space_refine on Mon Jun 23 14:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.map" model { file = "/net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wgv_32490/06_2025/7wgv_32490.cif" } resolution = 3.2 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= 0.140 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 120 5.16 5 C 17145 2.51 5 N 4398 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26931 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 3 Chain: "B" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 3 Chain: "C" Number of atoms: 8620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8620 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 51, 'TRANS': 1051} Chain breaks: 3 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: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 217 Unusual residues: {'BLR': 1, 'EIC': 1, 'NAG': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.14, per 1000 atoms: 0.56 Number of scatterers: 26931 At special positions: 0 Unit cell: (156.4, 144.16, 180.88, 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 120 16.00 O 5268 8.00 N 4398 7.00 C 17145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG 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 A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A 165 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 343 " " NAG A1310 " - " ASN A 17 " " NAG A1311 " - " ASN A 61 " " NAG A1312 " - " ASN A 149 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1074 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 165 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 343 " " NAG B1310 " - " ASN B 17 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 149 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C1098 " " NAG C1306 " - " ASN C 165 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 343 " " NAG C1310 " - " ASN C 17 " " NAG C1311 " - " ASN C 61 " " NAG C1312 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN B 717 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG N 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " Time building additional restraints: 7.39 Conformation dependent library (CDL) restraints added in 3.8 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 23.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.831A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.368A 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: 3.649A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.709A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.824A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.773A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.832A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.367A 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: 3.649A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.707A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.823A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.722A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.773A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1033 Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.832A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.586A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.368A 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: 3.649A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.707A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.824A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.723A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.773A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.511A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.527A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.443A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.389A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.622A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.628A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.699A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.510A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.526A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.443A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.389A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.113A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.623A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.622A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.700A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.269A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.423A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.511A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.526A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.039A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.444A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.298A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.390A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.114A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.623A 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: 4.699A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2883 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: 13.04 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.31: 4366 1.31 - 1.49: 11637 1.49 - 1.68: 11351 1.68 - 1.87: 168 1.87 - 2.06: 12 Bond restraints: 27534 Sorted by residual: bond pdb=" C1A BLR A1313 " pdb=" CHA BLR A1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.82e+02 bond pdb=" C1A BLR C1313 " pdb=" CHA BLR C1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.80e+02 bond pdb=" C1A BLR B1313 " pdb=" CHA BLR B1313 " ideal model delta sigma weight residual 1.498 2.057 -0.559 2.00e-02 2.50e+03 7.80e+02 bond pdb=" C2B BLR C1313 " pdb=" CMB BLR C1313 " ideal model delta sigma weight residual 1.489 1.953 -0.464 2.00e-02 2.50e+03 5.38e+02 bond pdb=" C2B BLR A1313 " pdb=" CMB BLR A1313 " ideal model delta sigma weight residual 1.489 1.953 -0.464 2.00e-02 2.50e+03 5.37e+02 ... (remaining 27529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.25: 37413 10.25 - 20.51: 21 20.51 - 30.76: 3 30.76 - 41.01: 9 41.01 - 51.27: 9 Bond angle restraints: 37455 Sorted by residual: angle pdb=" C2B BLR C1313 " pdb=" C1B BLR C1313 " pdb=" CHB BLR C1313 " ideal model delta sigma weight residual 123.24 174.51 -51.27 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C2B BLR A1313 " pdb=" C1B BLR A1313 " pdb=" CHB BLR A1313 " ideal model delta sigma weight residual 123.24 174.49 -51.25 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C2B BLR B1313 " pdb=" C1B BLR B1313 " pdb=" CHB BLR B1313 " ideal model delta sigma weight residual 123.24 174.46 -51.22 3.00e+00 1.11e-01 2.92e+02 angle pdb=" NB BLR A1313 " pdb=" C1B BLR A1313 " pdb=" CHB BLR A1313 " ideal model delta sigma weight residual 130.12 84.75 45.37 3.00e+00 1.11e-01 2.29e+02 angle pdb=" NB BLR C1313 " pdb=" C1B BLR C1313 " pdb=" CHB BLR C1313 " ideal model delta sigma weight residual 130.12 84.78 45.34 3.00e+00 1.11e-01 2.28e+02 ... (remaining 37450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15542 17.99 - 35.98: 1264 35.98 - 53.98: 234 53.98 - 71.97: 99 71.97 - 89.96: 42 Dihedral angle restraints: 17181 sinusoidal: 7551 harmonic: 9630 Sorted by residual: dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -161.53 75.53 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 17178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4134 0.103 - 0.207: 234 0.207 - 0.310: 6 0.310 - 0.413: 0 0.413 - 0.517: 6 Chirality restraints: 4380 Sorted by residual: chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 4377 not shown) Planarity restraints: 4806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.030 2.00e-02 2.50e+03 2.84e-02 1.01e+01 pdb=" CG ASN A 616 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 616 " -0.030 2.00e-02 2.50e+03 2.83e-02 1.00e+01 pdb=" CG ASN B 616 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B 616 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B 616 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 616 " 0.030 2.00e-02 2.50e+03 2.81e-02 9.89e+00 pdb=" CG ASN C 616 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 616 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 616 " -0.036 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.032 2.00e-02 2.50e+03 ... (remaining 4803 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 633 2.70 - 3.25: 24401 3.25 - 3.80: 38961 3.80 - 4.35: 51767 4.35 - 4.90: 89805 Nonbonded interactions: 205567 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.151 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.152 3.040 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.273 3.040 ... (remaining 205562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 65.790 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.180 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 0.559 27636 Z= 0.864 Angle : 1.319 51.266 37716 Z= 0.495 Chirality : 0.051 0.517 4380 Planarity : 0.003 0.031 4764 Dihedral : 14.424 89.961 10860 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.59 (0.14), residues: 3285 helix: 1.89 (0.21), residues: 726 sheet: 0.40 (0.18), residues: 768 loop : -1.83 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 152 HIS 0.002 0.000 HIS B1088 PHE 0.014 0.001 PHE A 486 TYR 0.014 0.001 TYR C1067 ARG 0.002 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 42) link_NAG-ASN : angle 4.87237 ( 126) link_BETA1-4 : bond 0.00293 ( 15) link_BETA1-4 : angle 0.88873 ( 45) hydrogen bonds : bond 0.12189 ( 1045) hydrogen bonds : angle 6.30149 ( 2883) SS BOND : bond 0.00732 ( 45) SS BOND : angle 2.52331 ( 90) covalent geometry : bond 0.01732 (27534) covalent geometry : angle 1.28662 (37455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.869 Fit side-chains revert: symmetry clash REVERT: B 111 ASP cc_start: 0.7011 (t0) cc_final: 0.6631 (t0) REVERT: C 111 ASP cc_start: 0.6694 (t0) cc_final: 0.6403 (t0) REVERT: C 177 MET cc_start: 0.8042 (ttp) cc_final: 0.7830 (ttm) REVERT: C 443 SER cc_start: 0.8097 (t) cc_final: 0.7729 (p) REVERT: C 781 VAL cc_start: 0.7561 (t) cc_final: 0.7234 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.4257 time to fit residues: 143.0048 Evaluate side-chains 133 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.0010 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 801 ASN A 895 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 801 ASN C 164 ASN C 493 GLN C 774 GLN C 801 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1011 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090000 restraints weight = 39463.868| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.11 r_work: 0.2976 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27636 Z= 0.149 Angle : 0.664 20.492 37716 Z= 0.314 Chirality : 0.047 0.420 4380 Planarity : 0.004 0.032 4764 Dihedral : 8.763 89.384 4965 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.45 % Allowed : 4.79 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.14), residues: 3285 helix: 1.82 (0.20), residues: 735 sheet: 0.29 (0.18), residues: 789 loop : -1.80 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.004 0.001 HIS C1088 PHE 0.011 0.001 PHE A 194 TYR 0.021 0.001 TYR C1138 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 42) link_NAG-ASN : angle 5.13502 ( 126) link_BETA1-4 : bond 0.00368 ( 15) link_BETA1-4 : angle 1.28310 ( 45) hydrogen bonds : bond 0.05029 ( 1045) hydrogen bonds : angle 5.42667 ( 2883) SS BOND : bond 0.00623 ( 45) SS BOND : angle 1.84347 ( 90) covalent geometry : bond 0.00347 (27534) covalent geometry : angle 0.58773 (37455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 3.027 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.8018 (m110) cc_final: 0.7494 (p0) REVERT: A 817 PHE cc_start: 0.6961 (t80) cc_final: 0.6749 (t80) REVERT: B 111 ASP cc_start: 0.8222 (t0) cc_final: 0.7667 (t0) REVERT: B 606 ASN cc_start: 0.8143 (m-40) cc_final: 0.7330 (p0) REVERT: B 817 PHE cc_start: 0.6799 (t80) cc_final: 0.6584 (t80) REVERT: C 111 ASP cc_start: 0.7798 (t0) cc_final: 0.7377 (t0) REVERT: C 177 MET cc_start: 0.8212 (ttp) cc_final: 0.7821 (ttm) REVERT: C 443 SER cc_start: 0.9114 (t) cc_final: 0.8808 (p) REVERT: C 731 MET cc_start: 0.8943 (ptm) cc_final: 0.8707 (ptp) REVERT: C 781 VAL cc_start: 0.7320 (t) cc_final: 0.6988 (t) outliers start: 13 outliers final: 5 residues processed: 159 average time/residue: 0.4117 time to fit residues: 104.4157 Evaluate side-chains 133 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 205 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 20 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN C 148 ASN C 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.115204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.086617 restraints weight = 39523.028| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.22 r_work: 0.2887 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27636 Z= 0.194 Angle : 0.660 20.847 37716 Z= 0.323 Chirality : 0.048 0.412 4380 Planarity : 0.004 0.033 4764 Dihedral : 7.887 88.916 4965 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.66 % Allowed : 7.22 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.14), residues: 3285 helix: 1.55 (0.20), residues: 744 sheet: 0.29 (0.18), residues: 792 loop : -1.81 (0.13), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS A1088 PHE 0.020 0.002 PHE B 906 TYR 0.021 0.002 TYR B1138 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 42) link_NAG-ASN : angle 4.96621 ( 126) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 1.33255 ( 45) hydrogen bonds : bond 0.05707 ( 1045) hydrogen bonds : angle 5.39045 ( 2883) SS BOND : bond 0.00667 ( 45) SS BOND : angle 2.34122 ( 90) covalent geometry : bond 0.00472 (27534) covalent geometry : angle 0.58359 (37455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 2.943 Fit side-chains revert: symmetry clash REVERT: A 606 ASN cc_start: 0.7987 (m110) cc_final: 0.7465 (p0) REVERT: A 1017 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7697 (tt0) REVERT: B 111 ASP cc_start: 0.8025 (t0) cc_final: 0.7518 (t0) REVERT: B 606 ASN cc_start: 0.8142 (m-40) cc_final: 0.7874 (m-40) REVERT: B 1050 MET cc_start: 0.8242 (ptp) cc_final: 0.7957 (ptp) REVERT: C 177 MET cc_start: 0.8477 (ttp) cc_final: 0.8093 (ttm) REVERT: C 443 SER cc_start: 0.9097 (t) cc_final: 0.8834 (p) outliers start: 19 outliers final: 9 residues processed: 162 average time/residue: 0.4311 time to fit residues: 108.9782 Evaluate side-chains 136 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 870 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 71 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 293 optimal weight: 4.9990 chunk 277 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 307 optimal weight: 0.0670 chunk 267 optimal weight: 0.8980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.087590 restraints weight = 39780.805| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.23 r_work: 0.2937 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27636 Z= 0.141 Angle : 0.616 20.712 37716 Z= 0.300 Chirality : 0.046 0.365 4380 Planarity : 0.003 0.033 4764 Dihedral : 7.428 86.751 4965 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.87 % Allowed : 8.54 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.62 (0.14), residues: 3285 helix: 1.57 (0.20), residues: 744 sheet: 0.22 (0.18), residues: 798 loop : -1.69 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS C1088 PHE 0.015 0.001 PHE B 194 TYR 0.020 0.001 TYR B1138 ARG 0.005 0.000 ARG C1019 Details of bonding type rmsd link_NAG-ASN : bond 0.00712 ( 42) link_NAG-ASN : angle 4.84833 ( 126) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.25947 ( 45) hydrogen bonds : bond 0.05184 ( 1045) hydrogen bonds : angle 5.27459 ( 2883) SS BOND : bond 0.00596 ( 45) SS BOND : angle 2.11394 ( 90) covalent geometry : bond 0.00333 (27534) covalent geometry : angle 0.53909 (37455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.8790 (t70) cc_final: 0.8273 (t70) REVERT: A 786 LYS cc_start: 0.8160 (pttm) cc_final: 0.7396 (tppt) REVERT: A 1019 ARG cc_start: 0.7902 (tmm160) cc_final: 0.7595 (ttp-170) REVERT: B 111 ASP cc_start: 0.8036 (t0) cc_final: 0.7544 (t0) REVERT: B 817 PHE cc_start: 0.7323 (t80) cc_final: 0.6996 (t80) REVERT: C 346 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8133 (mmm160) REVERT: C 443 SER cc_start: 0.9097 (t) cc_final: 0.8804 (p) REVERT: C 731 MET cc_start: 0.8603 (ptp) cc_final: 0.8400 (ptt) outliers start: 25 outliers final: 15 residues processed: 159 average time/residue: 0.4190 time to fit residues: 105.3562 Evaluate side-chains 145 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 87 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 138 optimal weight: 0.0040 chunk 24 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 318 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 493 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086602 restraints weight = 39678.380| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.22 r_work: 0.2916 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27636 Z= 0.166 Angle : 0.628 20.876 37716 Z= 0.308 Chirality : 0.046 0.330 4380 Planarity : 0.004 0.033 4764 Dihedral : 7.083 83.133 4965 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.32 % Allowed : 9.10 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.63 (0.14), residues: 3285 helix: 1.50 (0.20), residues: 747 sheet: 0.31 (0.18), residues: 840 loop : -1.77 (0.13), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 PHE 0.023 0.002 PHE A 133 TYR 0.023 0.001 TYR C1138 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 42) link_NAG-ASN : angle 4.80875 ( 126) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.24646 ( 45) hydrogen bonds : bond 0.05382 ( 1045) hydrogen bonds : angle 5.27325 ( 2883) SS BOND : bond 0.00696 ( 45) SS BOND : angle 2.36140 ( 90) covalent geometry : bond 0.00403 (27534) covalent geometry : angle 0.55107 (37455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7959 (pp) REVERT: A 574 ASP cc_start: 0.8784 (t70) cc_final: 0.8417 (t70) REVERT: A 786 LYS cc_start: 0.8068 (pttm) cc_final: 0.7312 (tppt) REVERT: A 1017 GLU cc_start: 0.8082 (tp30) cc_final: 0.7687 (tt0) REVERT: B 111 ASP cc_start: 0.7995 (t0) cc_final: 0.7491 (t0) REVERT: B 179 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7911 (pp) REVERT: C 346 ARG cc_start: 0.8376 (tpt90) cc_final: 0.8132 (mmm160) REVERT: C 443 SER cc_start: 0.9102 (t) cc_final: 0.8819 (p) REVERT: C 1076 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8307 (t) outliers start: 38 outliers final: 24 residues processed: 178 average time/residue: 0.4017 time to fit residues: 114.9082 Evaluate side-chains 159 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 218 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 266 optimal weight: 0.2980 chunk 238 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.085801 restraints weight = 39779.293| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.22 r_work: 0.2906 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27636 Z= 0.185 Angle : 0.643 20.996 37716 Z= 0.315 Chirality : 0.047 0.348 4380 Planarity : 0.004 0.034 4764 Dihedral : 6.942 78.338 4965 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.42 % Allowed : 9.69 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.68 (0.14), residues: 3285 helix: 1.45 (0.20), residues: 747 sheet: 0.28 (0.18), residues: 831 loop : -1.78 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 353 HIS 0.003 0.001 HIS C 49 PHE 0.016 0.002 PHE B 194 TYR 0.019 0.002 TYR B 365 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00726 ( 42) link_NAG-ASN : angle 4.85279 ( 126) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.24211 ( 45) hydrogen bonds : bond 0.05597 ( 1045) hydrogen bonds : angle 5.30889 ( 2883) SS BOND : bond 0.00693 ( 45) SS BOND : angle 2.43782 ( 90) covalent geometry : bond 0.00451 (27534) covalent geometry : angle 0.56598 (37455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7986 (pp) REVERT: A 574 ASP cc_start: 0.8776 (t70) cc_final: 0.8394 (t70) REVERT: A 786 LYS cc_start: 0.8179 (pttm) cc_final: 0.7344 (tppt) REVERT: A 882 ILE cc_start: 0.8798 (mt) cc_final: 0.8531 (mt) REVERT: A 979 ASP cc_start: 0.7957 (t0) cc_final: 0.7508 (t0) REVERT: A 1017 GLU cc_start: 0.8119 (tp30) cc_final: 0.7707 (tt0) REVERT: B 111 ASP cc_start: 0.8034 (t0) cc_final: 0.7532 (t0) REVERT: B 179 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7936 (pp) REVERT: B 986 LYS cc_start: 0.8589 (ptmm) cc_final: 0.8328 (ptmm) REVERT: B 1017 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7826 (tt0) REVERT: C 244 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8076 (pp) REVERT: C 346 ARG cc_start: 0.8374 (tpt90) cc_final: 0.8169 (mmm160) REVERT: C 443 SER cc_start: 0.9105 (t) cc_final: 0.8823 (p) REVERT: C 1017 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7931 (tt0) REVERT: C 1076 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8307 (p) outliers start: 41 outliers final: 29 residues processed: 180 average time/residue: 0.3967 time to fit residues: 114.3245 Evaluate side-chains 167 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 153 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 chunk 13 optimal weight: 8.9990 chunk 329 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 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 = 0.3480 r_free = 0.3480 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086892 restraints weight = 39566.861| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.22 r_work: 0.2933 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27636 Z= 0.142 Angle : 0.609 20.919 37716 Z= 0.298 Chirality : 0.046 0.395 4380 Planarity : 0.003 0.035 4764 Dihedral : 6.702 70.836 4965 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.46 % Allowed : 9.83 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.58 (0.14), residues: 3285 helix: 1.55 (0.20), residues: 744 sheet: 0.26 (0.18), residues: 846 loop : -1.69 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS A1088 PHE 0.015 0.001 PHE B 194 TYR 0.019 0.001 TYR B 365 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 42) link_NAG-ASN : angle 4.76375 ( 126) link_BETA1-4 : bond 0.00378 ( 15) link_BETA1-4 : angle 1.20563 ( 45) hydrogen bonds : bond 0.05140 ( 1045) hydrogen bonds : angle 5.21506 ( 2883) SS BOND : bond 0.00643 ( 45) SS BOND : angle 2.09953 ( 90) covalent geometry : bond 0.00336 (27534) covalent geometry : angle 0.53328 (37455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7983 (pp) REVERT: A 574 ASP cc_start: 0.8780 (t70) cc_final: 0.8417 (t70) REVERT: A 786 LYS cc_start: 0.8228 (pttm) cc_final: 0.7365 (tppt) REVERT: A 1017 GLU cc_start: 0.8054 (tp30) cc_final: 0.7667 (tt0) REVERT: B 111 ASP cc_start: 0.7990 (t0) cc_final: 0.7544 (t0) REVERT: B 179 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7906 (pp) REVERT: B 986 LYS cc_start: 0.8633 (ptmm) cc_final: 0.8416 (ptmm) REVERT: C 443 SER cc_start: 0.9104 (t) cc_final: 0.8797 (p) REVERT: C 1076 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8244 (p) outliers start: 42 outliers final: 31 residues processed: 182 average time/residue: 0.4020 time to fit residues: 116.6247 Evaluate side-chains 171 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 155 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 252 optimal weight: 0.2980 chunk 286 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 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 = 0.3467 r_free = 0.3467 target = 0.114301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085885 restraints weight = 39923.624| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.22 r_work: 0.2899 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27636 Z= 0.171 Angle : 0.628 20.977 37716 Z= 0.308 Chirality : 0.047 0.388 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.645 69.269 4965 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.42 % Allowed : 10.17 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.62 (0.14), residues: 3285 helix: 1.51 (0.20), residues: 747 sheet: 0.20 (0.18), residues: 858 loop : -1.71 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS A1088 PHE 0.015 0.001 PHE B 194 TYR 0.019 0.001 TYR B 365 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 42) link_NAG-ASN : angle 4.76265 ( 126) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.21427 ( 45) hydrogen bonds : bond 0.05421 ( 1045) hydrogen bonds : angle 5.24775 ( 2883) SS BOND : bond 0.00730 ( 45) SS BOND : angle 2.17171 ( 90) covalent geometry : bond 0.00416 (27534) covalent geometry : angle 0.55472 (37455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 5.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8006 (pp) REVERT: A 214 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7731 (mmm-85) REVERT: A 574 ASP cc_start: 0.8774 (t70) cc_final: 0.8450 (t70) REVERT: A 786 LYS cc_start: 0.8255 (pttm) cc_final: 0.7390 (tppt) REVERT: A 979 ASP cc_start: 0.7979 (t0) cc_final: 0.7527 (t0) REVERT: A 1017 GLU cc_start: 0.8120 (tp30) cc_final: 0.7743 (tt0) REVERT: B 111 ASP cc_start: 0.8017 (t0) cc_final: 0.7517 (t0) REVERT: B 179 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7924 (pp) REVERT: B 986 LYS cc_start: 0.8505 (ptmm) cc_final: 0.8261 (ptmm) REVERT: B 1017 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7831 (tt0) REVERT: C 244 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8078 (pp) REVERT: C 443 SER cc_start: 0.9105 (t) cc_final: 0.8816 (p) REVERT: C 1017 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7907 (tt0) REVERT: C 1076 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8279 (p) outliers start: 41 outliers final: 31 residues processed: 178 average time/residue: 0.5038 time to fit residues: 143.5219 Evaluate side-chains 173 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 79 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 101 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 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 = 0.3477 r_free = 0.3477 target = 0.115071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086686 restraints weight = 39815.027| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.22 r_work: 0.2912 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 27636 Z= 0.147 Angle : 0.621 20.911 37716 Z= 0.305 Chirality : 0.046 0.336 4380 Planarity : 0.003 0.037 4764 Dihedral : 6.577 69.219 4965 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.32 % Allowed : 10.62 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.14), residues: 3285 helix: 1.57 (0.20), residues: 747 sheet: 0.30 (0.18), residues: 855 loop : -1.71 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.002 0.001 HIS A1088 PHE 0.021 0.001 PHE C 133 TYR 0.019 0.001 TYR B 365 ARG 0.006 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 42) link_NAG-ASN : angle 4.70373 ( 126) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.19519 ( 45) hydrogen bonds : bond 0.05151 ( 1045) hydrogen bonds : angle 5.22338 ( 2883) SS BOND : bond 0.00675 ( 45) SS BOND : angle 2.44024 ( 90) covalent geometry : bond 0.00353 (27534) covalent geometry : angle 0.54625 (37455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 574 ASP cc_start: 0.8773 (t70) cc_final: 0.8457 (t70) REVERT: A 786 LYS cc_start: 0.8270 (pttm) cc_final: 0.7401 (tppt) REVERT: A 1017 GLU cc_start: 0.8091 (tp30) cc_final: 0.7711 (tt0) REVERT: B 111 ASP cc_start: 0.7947 (t0) cc_final: 0.7487 (t0) REVERT: B 179 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7903 (pp) REVERT: B 986 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8411 (ptmm) REVERT: B 1017 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7835 (tt0) REVERT: C 244 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8066 (pp) REVERT: C 319 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8566 (mtp85) REVERT: C 443 SER cc_start: 0.9103 (t) cc_final: 0.8794 (p) REVERT: C 1017 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7922 (tt0) REVERT: C 1076 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8279 (p) outliers start: 38 outliers final: 34 residues processed: 176 average time/residue: 0.4008 time to fit residues: 112.4318 Evaluate side-chains 177 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 0 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 328 optimal weight: 0.2980 chunk 205 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 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 = 0.3441 r_free = 0.3441 target = 0.112459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.083837 restraints weight = 40083.378| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.23 r_work: 0.2884 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 27636 Z= 0.243 Angle : 0.698 21.201 37716 Z= 0.345 Chirality : 0.049 0.331 4380 Planarity : 0.004 0.038 4764 Dihedral : 6.839 72.831 4965 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.32 % Allowed : 10.66 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.79 (0.14), residues: 3285 helix: 1.39 (0.20), residues: 744 sheet: 0.13 (0.18), residues: 852 loop : -1.84 (0.13), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.004 0.001 HIS C 49 PHE 0.019 0.002 PHE B1121 TYR 0.020 0.002 TYR B 365 ARG 0.008 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 42) link_NAG-ASN : angle 4.87632 ( 126) link_BETA1-4 : bond 0.00333 ( 15) link_BETA1-4 : angle 1.26250 ( 45) hydrogen bonds : bond 0.06238 ( 1045) hydrogen bonds : angle 5.41557 ( 2883) SS BOND : bond 0.00793 ( 45) SS BOND : angle 2.83416 ( 90) covalent geometry : bond 0.00601 (27534) covalent geometry : angle 0.62442 (37455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (pp) REVERT: A 574 ASP cc_start: 0.8770 (t70) cc_final: 0.8446 (t70) REVERT: A 786 LYS cc_start: 0.8404 (pttm) cc_final: 0.7666 (tppt) REVERT: A 882 ILE cc_start: 0.8843 (mt) cc_final: 0.8562 (mt) REVERT: A 979 ASP cc_start: 0.8008 (t0) cc_final: 0.7545 (t0) REVERT: A 1017 GLU cc_start: 0.8148 (tp30) cc_final: 0.7790 (tt0) REVERT: B 179 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7939 (pp) REVERT: B 986 LYS cc_start: 0.8587 (ptmm) cc_final: 0.8354 (ptmm) REVERT: C 244 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8092 (pp) REVERT: C 443 SER cc_start: 0.9056 (t) cc_final: 0.8786 (p) REVERT: C 817 PHE cc_start: 0.7510 (t80) cc_final: 0.7289 (t80) REVERT: C 1002 GLN cc_start: 0.7429 (tp40) cc_final: 0.7137 (tt0) REVERT: C 1017 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7934 (tt0) REVERT: C 1076 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8337 (p) outliers start: 38 outliers final: 33 residues processed: 175 average time/residue: 0.4143 time to fit residues: 115.5673 Evaluate side-chains 176 residues out of total 2880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1076 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 322 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 279 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 272 optimal weight: 0.7980 chunk 149 optimal weight: 0.0070 chunk 184 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1002 GLN C 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087968 restraints weight = 39641.856| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.22 r_work: 0.2934 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27636 Z= 0.113 Angle : 0.602 20.826 37716 Z= 0.295 Chirality : 0.046 0.301 4380 Planarity : 0.003 0.036 4764 Dihedral : 6.397 70.401 4965 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.25 % Allowed : 10.90 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 3285 helix: 1.61 (0.20), residues: 744 sheet: 0.32 (0.18), residues: 834 loop : -1.69 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.003 0.000 HIS B 655 PHE 0.018 0.001 PHE C 133 TYR 0.020 0.001 TYR B 365 ARG 0.008 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 42) link_NAG-ASN : angle 4.61606 ( 126) link_BETA1-4 : bond 0.00427 ( 15) link_BETA1-4 : angle 1.17750 ( 45) hydrogen bonds : bond 0.04697 ( 1045) hydrogen bonds : angle 5.17068 ( 2883) SS BOND : bond 0.00608 ( 45) SS BOND : angle 2.07624 ( 90) covalent geometry : bond 0.00252 (27534) covalent geometry : angle 0.52986 (37455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11304.14 seconds wall clock time: 199 minutes 23.80 seconds (11963.80 seconds total)