Starting phenix.real_space_refine on Sun Jun 22 05:19:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.map" model { file = "/net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elq_48159/06_2025/9elq_48159.cif" } resolution = 2.64 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= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16254 2.51 5 N 4143 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25479 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8233 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "B" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8233 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "C" Number of atoms: 8233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8233 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 56, 'TRANS': 993} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 16.62, per 1000 atoms: 0.65 Number of scatterers: 25479 At special positions: 0 Unit cell: (137.856, 138.574, 186.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4968 8.00 N 4143 7.00 C 16254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.02 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 D 2 " - " BMA D 3 " " 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 H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 354 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 354 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 30 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 354 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 30 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 282 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 282 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 3.2 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 39 sheets defined 27.2% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.973A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.433A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.621A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.025A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.684A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.408A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.584A pdb=" N LEU A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.973A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.432A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.621A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.025A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.684A 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.408A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1149 removed outlier: 3.584A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.972A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.433A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.621A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.024A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.684A 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.408A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.584A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C1149 " --> pdb=" O LEU C1145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.717A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.361A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.815A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 172 removed outlier: 7.329A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.426A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.327A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.360A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.587A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.643A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.764A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.718A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.361A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.816A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 163 through 172 removed outlier: 7.329A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.426A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.192A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.586A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 790 removed outlier: 3.643A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.764A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 26 through 28 removed outlier: 5.717A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.816A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 163 through 172 removed outlier: 7.329A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.191A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.561A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.587A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.763A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 2985 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: 11.63 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4610 1.33 - 1.45: 7154 1.45 - 1.58: 14153 1.58 - 1.70: 6 1.70 - 1.83: 144 Bond restraints: 26067 Sorted by residual: bond pdb=" N PHE B 855 " pdb=" CA PHE B 855 " ideal model delta sigma weight residual 1.462 1.510 -0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" N PHE C 855 " pdb=" CA PHE C 855 " ideal model delta sigma weight residual 1.462 1.510 -0.048 1.23e-02 6.61e+03 1.52e+01 bond pdb=" N PHE A 855 " pdb=" CA PHE A 855 " ideal model delta sigma weight residual 1.462 1.510 -0.048 1.23e-02 6.61e+03 1.51e+01 bond pdb=" N THR C 29 " pdb=" CA THR C 29 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.33e-02 5.65e+03 1.34e+01 bond pdb=" N THR A 29 " pdb=" CA THR A 29 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.33e-02 5.65e+03 1.34e+01 ... (remaining 26062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 34686 3.90 - 7.80: 699 7.80 - 11.70: 66 11.70 - 15.60: 6 15.60 - 19.50: 3 Bond angle restraints: 35460 Sorted by residual: angle pdb=" C PHE A 855 " pdb=" CA PHE A 855 " pdb=" CB PHE A 855 " ideal model delta sigma weight residual 111.91 92.41 19.50 1.52e+00 4.33e-01 1.65e+02 angle pdb=" C PHE C 855 " pdb=" CA PHE C 855 " pdb=" CB PHE C 855 " ideal model delta sigma weight residual 111.91 92.42 19.49 1.52e+00 4.33e-01 1.64e+02 angle pdb=" C PHE B 855 " pdb=" CA PHE B 855 " pdb=" CB PHE B 855 " ideal model delta sigma weight residual 111.91 92.42 19.49 1.52e+00 4.33e-01 1.64e+02 angle pdb=" O ASP C1139 " pdb=" C ASP C1139 " pdb=" N PRO C1140 " ideal model delta sigma weight residual 121.23 115.58 5.65 8.10e-01 1.52e+00 4.86e+01 angle pdb=" O ASP B1139 " pdb=" C ASP B1139 " pdb=" N PRO B1140 " ideal model delta sigma weight residual 121.23 115.59 5.64 8.10e-01 1.52e+00 4.85e+01 ... (remaining 35455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.08: 15519 21.08 - 42.15: 495 42.15 - 63.23: 164 63.23 - 84.30: 64 84.30 - 105.38: 39 Dihedral angle restraints: 16281 sinusoidal: 7107 harmonic: 9174 Sorted by residual: dihedral pdb=" C PHE C 855 " pdb=" N PHE C 855 " pdb=" CA PHE C 855 " pdb=" CB PHE C 855 " ideal model delta harmonic sigma weight residual -122.60 -105.89 -16.71 0 2.50e+00 1.60e-01 4.47e+01 dihedral pdb=" C PHE B 855 " pdb=" N PHE B 855 " pdb=" CA PHE B 855 " pdb=" CB PHE B 855 " ideal model delta harmonic sigma weight residual -122.60 -105.91 -16.69 0 2.50e+00 1.60e-01 4.46e+01 dihedral pdb=" C PHE A 855 " pdb=" N PHE A 855 " pdb=" CA PHE A 855 " pdb=" CB PHE A 855 " ideal model delta harmonic sigma weight residual -122.60 -105.91 -16.69 0 2.50e+00 1.60e-01 4.46e+01 ... (remaining 16278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 3884 0.130 - 0.260: 271 0.260 - 0.391: 15 0.391 - 0.521: 3 0.521 - 0.651: 3 Chirality restraints: 4176 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 4173 not shown) Planarity restraints: 4533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.152 2.00e-02 2.50e+03 2.01e-01 5.04e+02 pdb=" CG ASN C 331 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.342 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.152 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" CG ASN A 331 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.342 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.237 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 30 " -0.161 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" CG ASN B 30 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN B 30 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 30 " 0.337 2.00e-02 2.50e+03 pdb=" C1 NAG B1307 " -0.238 2.00e-02 2.50e+03 ... (remaining 4530 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 9 2.15 - 2.84: 7698 2.84 - 3.53: 34274 3.53 - 4.21: 60294 4.21 - 4.90: 102974 Nonbonded interactions: 205249 Sorted by model distance: nonbonded pdb=" CD2 TYR A 28 " pdb=" CE2 PHE A 32 " model vdw 1.468 3.640 nonbonded pdb=" CD2 TYR C 28 " pdb=" CE2 PHE C 32 " model vdw 1.468 3.640 nonbonded pdb=" CD2 TYR B 28 " pdb=" CE2 PHE B 32 " model vdw 1.469 3.640 nonbonded pdb=" CE2 TYR A 28 " pdb=" CE2 PHE A 32 " model vdw 1.934 3.640 nonbonded pdb=" CE2 TYR C 28 " pdb=" CE2 PHE C 32 " model vdw 1.934 3.640 ... (remaining 205244 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 124.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.170 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 61.800 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.008 0.096 26163 Z= 0.375 Angle : 1.360 19.495 35709 Z= 0.796 Chirality : 0.073 0.651 4176 Planarity : 0.015 0.340 4497 Dihedral : 13.791 105.376 10260 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.28 % Cbeta Deviations : 0.30 % 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: 0.61 (0.14), residues: 3108 helix: 1.09 (0.18), residues: 714 sheet: 1.16 (0.20), residues: 591 loop : -0.08 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.007 TRP A 452 HIS 0.011 0.002 HIS B1048 PHE 0.040 0.004 PHE B 371 TYR 0.044 0.004 TYR A 160 ARG 0.024 0.002 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 36) link_NAG-ASN : angle 4.29856 ( 108) link_BETA1-4 : bond 0.01059 ( 21) link_BETA1-4 : angle 4.05693 ( 63) hydrogen bonds : bond 0.13520 ( 1043) hydrogen bonds : angle 7.45585 ( 2985) SS BOND : bond 0.00616 ( 39) SS BOND : angle 1.80194 ( 78) covalent geometry : bond 0.00761 (26067) covalent geometry : angle 1.33002 (35460) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 419 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8239 (m) cc_final: 0.7970 (p) REVERT: A 177 MET cc_start: 0.2434 (mmm) cc_final: 0.1837 (pmm) REVERT: A 190 ARG cc_start: 0.7500 (mtt90) cc_final: 0.6624 (mtm-85) REVERT: A 205 SER cc_start: 0.9116 (p) cc_final: 0.8763 (t) REVERT: A 514 SER cc_start: 0.7613 (m) cc_final: 0.7329 (p) REVERT: A 646 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7578 (mtt90) REVERT: A 780 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7735 (tt0) REVERT: A 821 LEU cc_start: 0.8178 (tp) cc_final: 0.7972 (mp) REVERT: A 921 LYS cc_start: 0.8543 (ttmm) cc_final: 0.7835 (mptt) REVERT: A 964 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7427 (mtmm) REVERT: A 994 ASP cc_start: 0.7625 (t70) cc_final: 0.7217 (m-30) REVERT: A 1017 GLU cc_start: 0.8686 (tt0) cc_final: 0.8482 (tt0) REVERT: A 1038 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8001 (mptp) REVERT: B 47 VAL cc_start: 0.8253 (m) cc_final: 0.8011 (p) REVERT: B 177 MET cc_start: 0.2228 (mmm) cc_final: 0.1675 (pmm) REVERT: B 190 ARG cc_start: 0.7470 (mtt90) cc_final: 0.6582 (mtm-85) REVERT: B 205 SER cc_start: 0.9162 (p) cc_final: 0.8708 (t) REVERT: B 514 SER cc_start: 0.7643 (m) cc_final: 0.7383 (p) REVERT: B 569 ILE cc_start: 0.8152 (mp) cc_final: 0.7946 (tp) REVERT: B 586 ASP cc_start: 0.7759 (m-30) cc_final: 0.7487 (m-30) REVERT: B 646 ARG cc_start: 0.8092 (mmm-85) cc_final: 0.7510 (mtt90) REVERT: B 780 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7795 (tt0) REVERT: B 821 LEU cc_start: 0.8105 (tp) cc_final: 0.7792 (mp) REVERT: B 921 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8161 (ttpp) REVERT: B 994 ASP cc_start: 0.7595 (t70) cc_final: 0.7368 (m-30) REVERT: B 1017 GLU cc_start: 0.8707 (tt0) cc_final: 0.8468 (tt0) REVERT: B 1038 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8132 (mppt) REVERT: B 1100 THR cc_start: 0.8397 (p) cc_final: 0.8197 (t) REVERT: C 47 VAL cc_start: 0.8222 (m) cc_final: 0.7950 (p) REVERT: C 177 MET cc_start: 0.2236 (mmm) cc_final: 0.1739 (pmm) REVERT: C 190 ARG cc_start: 0.7563 (mtt90) cc_final: 0.6633 (mtm-85) REVERT: C 205 SER cc_start: 0.9184 (p) cc_final: 0.8795 (t) REVERT: C 269 TYR cc_start: 0.8128 (m-80) cc_final: 0.7851 (m-80) REVERT: C 355 ARG cc_start: 0.6728 (ttt90) cc_final: 0.6509 (ttt90) REVERT: C 514 SER cc_start: 0.7645 (m) cc_final: 0.7311 (p) REVERT: C 641 ASN cc_start: 0.7491 (p0) cc_final: 0.7179 (p0) REVERT: C 646 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7535 (mtt90) REVERT: C 780 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7831 (tt0) REVERT: C 821 LEU cc_start: 0.8122 (tp) cc_final: 0.7812 (mp) REVERT: C 869 MET cc_start: 0.9389 (mtt) cc_final: 0.9180 (mtt) REVERT: C 921 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8182 (ttpp) REVERT: C 964 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7478 (mtmt) REVERT: C 994 ASP cc_start: 0.7554 (t70) cc_final: 0.7279 (m-30) REVERT: C 1038 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8093 (mppt) REVERT: C 1045 LYS cc_start: 0.8465 (tptt) cc_final: 0.8261 (tptp) outliers start: 3 outliers final: 1 residues processed: 422 average time/residue: 1.3328 time to fit residues: 665.2279 Evaluate side-chains 256 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 1038 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 246 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 0.0870 chunk 183 optimal weight: 0.9980 chunk 286 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 196 ASN A 564 GLN A1005 GLN B 115 GLN B 564 GLN C 115 GLN C 564 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.210789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134969 restraints weight = 25748.699| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3297 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26163 Z= 0.153 Angle : 0.754 16.662 35709 Z= 0.369 Chirality : 0.051 0.523 4176 Planarity : 0.005 0.051 4497 Dihedral : 9.042 69.116 4568 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.74 % Favored : 98.20 % Rotamer: Outliers : 2.17 % Allowed : 7.87 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.14), residues: 3108 helix: 2.46 (0.19), residues: 687 sheet: 0.90 (0.19), residues: 630 loop : -0.25 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 452 HIS 0.005 0.001 HIS A1048 PHE 0.025 0.002 PHE B 855 TYR 0.022 0.002 TYR A1067 ARG 0.010 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 36) link_NAG-ASN : angle 5.88007 ( 108) link_BETA1-4 : bond 0.00759 ( 21) link_BETA1-4 : angle 3.44366 ( 63) hydrogen bonds : bond 0.05453 ( 1043) hydrogen bonds : angle 6.13533 ( 2985) SS BOND : bond 0.00260 ( 39) SS BOND : angle 1.03939 ( 78) covalent geometry : bond 0.00333 (26067) covalent geometry : angle 0.66653 (35460) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7699 (m-80) cc_final: 0.7303 (m-80) REVERT: A 153 MET cc_start: 0.2988 (mmt) cc_final: 0.1469 (ttm) REVERT: A 177 MET cc_start: 0.2504 (mmm) cc_final: 0.1738 (pmm) REVERT: A 190 ARG cc_start: 0.7656 (mtt90) cc_final: 0.6718 (mtm-85) REVERT: A 514 SER cc_start: 0.7735 (m) cc_final: 0.7445 (p) REVERT: A 646 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7887 (mtt90) REVERT: A 780 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8198 (mm-30) REVERT: A 821 LEU cc_start: 0.8326 (tp) cc_final: 0.8058 (mp) REVERT: A 964 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7783 (mtpt) REVERT: A 995 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7327 (mtp180) REVERT: A 1119 ASN cc_start: 0.8295 (m-40) cc_final: 0.7969 (m-40) REVERT: B 65 PHE cc_start: 0.7756 (m-80) cc_final: 0.7365 (m-80) REVERT: B 177 MET cc_start: 0.2337 (mmm) cc_final: 0.1523 (pmm) REVERT: B 190 ARG cc_start: 0.7661 (mtt90) cc_final: 0.6723 (mtm-85) REVERT: B 205 SER cc_start: 0.9041 (p) cc_final: 0.8767 (t) REVERT: B 514 SER cc_start: 0.7760 (m) cc_final: 0.7485 (p) REVERT: B 569 ILE cc_start: 0.8025 (mp) cc_final: 0.7777 (tp) REVERT: B 646 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7861 (mtm180) REVERT: B 780 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8193 (mm-30) REVERT: B 821 LEU cc_start: 0.8254 (tp) cc_final: 0.7953 (mp) REVERT: B 921 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8082 (mptt) REVERT: B 964 LYS cc_start: 0.8421 (mmmm) cc_final: 0.7812 (mtpt) REVERT: C 177 MET cc_start: 0.2484 (mmm) cc_final: 0.1649 (pmm) REVERT: C 190 ARG cc_start: 0.7766 (mtt90) cc_final: 0.6815 (mtm-85) REVERT: C 205 SER cc_start: 0.9095 (p) cc_final: 0.8875 (t) REVERT: C 269 TYR cc_start: 0.8185 (m-80) cc_final: 0.7952 (m-80) REVERT: C 355 ARG cc_start: 0.6861 (ttt90) cc_final: 0.6012 (ttt-90) REVERT: C 514 SER cc_start: 0.7761 (m) cc_final: 0.7457 (p) REVERT: C 646 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.7845 (mtt90) REVERT: C 780 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7852 (pt0) REVERT: C 821 LEU cc_start: 0.8245 (tp) cc_final: 0.7967 (mp) REVERT: C 921 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8279 (ttpp) REVERT: C 964 LYS cc_start: 0.8468 (mmmt) cc_final: 0.7845 (mtpt) REVERT: C 994 ASP cc_start: 0.7685 (t70) cc_final: 0.7446 (t70) outliers start: 60 outliers final: 21 residues processed: 301 average time/residue: 1.0517 time to fit residues: 380.2600 Evaluate side-chains 244 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 255 optimal weight: 5.9990 chunk 269 optimal weight: 0.0470 chunk 99 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 196 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1005 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.209384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133439 restraints weight = 25563.256| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.21 r_work: 0.3276 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26163 Z= 0.136 Angle : 0.660 18.400 35709 Z= 0.323 Chirality : 0.049 0.579 4176 Planarity : 0.004 0.033 4497 Dihedral : 6.592 56.829 4556 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 2.31 % Allowed : 8.99 % Favored : 88.70 % 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: 3108 helix: 2.50 (0.19), residues: 693 sheet: 0.59 (0.19), residues: 633 loop : -0.41 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 452 HIS 0.005 0.001 HIS A 954 PHE 0.027 0.002 PHE C1075 TYR 0.024 0.001 TYR A1067 ARG 0.007 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 36) link_NAG-ASN : angle 4.88550 ( 108) link_BETA1-4 : bond 0.00757 ( 21) link_BETA1-4 : angle 3.10339 ( 63) hydrogen bonds : bond 0.04842 ( 1043) hydrogen bonds : angle 5.67143 ( 2985) SS BOND : bond 0.00237 ( 39) SS BOND : angle 0.81725 ( 78) covalent geometry : bond 0.00297 (26067) covalent geometry : angle 0.58927 (35460) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 5.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7823 (m-80) cc_final: 0.7571 (m-80) REVERT: A 153 MET cc_start: 0.3076 (mmt) cc_final: 0.1449 (ttm) REVERT: A 177 MET cc_start: 0.2661 (mmm) cc_final: 0.1855 (pmm) REVERT: A 190 ARG cc_start: 0.7749 (mtt90) cc_final: 0.6830 (mtm-85) REVERT: A 514 SER cc_start: 0.7828 (m) cc_final: 0.7567 (p) REVERT: A 646 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.7994 (mtt90) REVERT: A 658 ASN cc_start: 0.7834 (m-40) cc_final: 0.7631 (m-40) REVERT: A 821 LEU cc_start: 0.8356 (tp) cc_final: 0.8076 (mp) REVERT: A 964 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7906 (mtpt) REVERT: A 994 ASP cc_start: 0.7840 (t70) cc_final: 0.7492 (t70) REVERT: A 995 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7334 (mtp180) REVERT: B 177 MET cc_start: 0.2471 (mmm) cc_final: 0.1671 (pmm) REVERT: B 190 ARG cc_start: 0.7794 (mtt90) cc_final: 0.6895 (mtm-85) REVERT: B 206 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8254 (tptt) REVERT: B 514 SER cc_start: 0.7805 (m) cc_final: 0.7591 (p) REVERT: B 554 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7287 (ttpp) REVERT: B 646 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.7957 (mtt90) REVERT: B 740 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (ttt) REVERT: B 821 LEU cc_start: 0.8295 (tp) cc_final: 0.7982 (mp) REVERT: B 921 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8064 (mptt) REVERT: B 964 LYS cc_start: 0.8466 (mmmm) cc_final: 0.7862 (mtpt) REVERT: B 1119 ASN cc_start: 0.8305 (m-40) cc_final: 0.7890 (m-40) REVERT: C 177 MET cc_start: 0.2614 (mmm) cc_final: 0.1880 (pmm) REVERT: C 190 ARG cc_start: 0.7854 (mtt90) cc_final: 0.6886 (mtm-85) REVERT: C 206 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8190 (tmtm) REVERT: C 269 TYR cc_start: 0.8238 (m-80) cc_final: 0.7969 (m-80) REVERT: C 355 ARG cc_start: 0.6901 (ttt90) cc_final: 0.6183 (ttt-90) REVERT: C 514 SER cc_start: 0.7875 (m) cc_final: 0.7570 (p) REVERT: C 554 LYS cc_start: 0.7398 (tmmt) cc_final: 0.7155 (tmmt) REVERT: C 646 ARG cc_start: 0.8414 (mmm-85) cc_final: 0.7878 (mtt90) REVERT: C 780 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7851 (pt0) REVERT: C 787 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: C 811 LYS cc_start: 0.6312 (mttp) cc_final: 0.5510 (ptpt) REVERT: C 821 LEU cc_start: 0.8301 (tp) cc_final: 0.8004 (mp) REVERT: C 869 MET cc_start: 0.9395 (mtt) cc_final: 0.9168 (mtt) REVERT: C 921 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8303 (ttpp) REVERT: C 964 LYS cc_start: 0.8569 (mmmt) cc_final: 0.7921 (mtpt) REVERT: C 994 ASP cc_start: 0.7741 (t70) cc_final: 0.7486 (t70) REVERT: C 1119 ASN cc_start: 0.8296 (m-40) cc_final: 0.7926 (m-40) outliers start: 64 outliers final: 27 residues processed: 283 average time/residue: 1.3707 time to fit residues: 472.7839 Evaluate side-chains 256 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 155 optimal weight: 9.9990 chunk 182 optimal weight: 0.0970 chunk 16 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 chunk 209 optimal weight: 0.0060 chunk 231 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.210727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133507 restraints weight = 25924.119| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.22 r_work: 0.3306 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26163 Z= 0.111 Angle : 0.577 12.003 35709 Z= 0.286 Chirality : 0.045 0.293 4176 Planarity : 0.004 0.035 4497 Dihedral : 5.742 55.846 4556 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.96 % Favored : 97.84 % Rotamer: Outliers : 1.73 % Allowed : 10.36 % Favored : 87.90 % 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: 0.67 (0.14), residues: 3108 helix: 2.71 (0.19), residues: 678 sheet: 0.51 (0.19), residues: 633 loop : -0.48 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 452 HIS 0.005 0.001 HIS A 954 PHE 0.016 0.001 PHE B 65 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00859 ( 36) link_NAG-ASN : angle 4.11494 ( 108) link_BETA1-4 : bond 0.00728 ( 21) link_BETA1-4 : angle 2.75475 ( 63) hydrogen bonds : bond 0.04216 ( 1043) hydrogen bonds : angle 5.37384 ( 2985) SS BOND : bond 0.00155 ( 39) SS BOND : angle 0.68666 ( 78) covalent geometry : bond 0.00233 (26067) covalent geometry : angle 0.51882 (35460) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1807 (OUTLIER) cc_final: 0.1255 (mttp) REVERT: A 177 MET cc_start: 0.2756 (mmm) cc_final: 0.1951 (pmm) REVERT: A 190 ARG cc_start: 0.7770 (mtt90) cc_final: 0.6838 (mtm-85) REVERT: A 382 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7828 (m) REVERT: A 514 SER cc_start: 0.7863 (m) cc_final: 0.7587 (p) REVERT: A 646 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.7995 (mtt90) REVERT: A 786 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7448 (mttp) REVERT: A 821 LEU cc_start: 0.8332 (tp) cc_final: 0.8053 (mp) REVERT: A 964 LYS cc_start: 0.8556 (mmmt) cc_final: 0.7907 (mtpt) REVERT: A 994 ASP cc_start: 0.7756 (t70) cc_final: 0.7468 (t70) REVERT: A 995 ARG cc_start: 0.7808 (mtt90) cc_final: 0.7295 (mtp180) REVERT: B 177 MET cc_start: 0.2475 (mmm) cc_final: 0.1733 (pmm) REVERT: B 190 ARG cc_start: 0.7828 (mtt90) cc_final: 0.6957 (mtm-85) REVERT: B 382 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7804 (m) REVERT: B 554 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7245 (tptp) REVERT: B 569 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 646 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.7961 (mtt90) REVERT: B 787 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8226 (mm-40) REVERT: B 821 LEU cc_start: 0.8301 (tp) cc_final: 0.8008 (mp) REVERT: B 916 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8358 (tt) REVERT: B 921 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8104 (mptt) REVERT: B 964 LYS cc_start: 0.8427 (mmmm) cc_final: 0.7804 (mtpt) REVERT: B 995 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7356 (mtp180) REVERT: C 177 MET cc_start: 0.2625 (mmm) cc_final: 0.1928 (pmm) REVERT: C 190 ARG cc_start: 0.7864 (mtt90) cc_final: 0.6859 (mtm-85) REVERT: C 269 TYR cc_start: 0.8197 (m-80) cc_final: 0.7952 (m-80) REVERT: C 355 ARG cc_start: 0.6884 (ttt90) cc_final: 0.6268 (ttt-90) REVERT: C 382 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7861 (m) REVERT: C 514 SER cc_start: 0.7814 (m) cc_final: 0.7531 (p) REVERT: C 646 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7891 (mtt90) REVERT: C 787 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8180 (mm-40) REVERT: C 811 LYS cc_start: 0.6342 (mttp) cc_final: 0.5491 (ptpt) REVERT: C 821 LEU cc_start: 0.8286 (tp) cc_final: 0.8001 (mp) REVERT: C 921 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8303 (ttpp) REVERT: C 964 LYS cc_start: 0.8542 (mmmt) cc_final: 0.7857 (mtpt) REVERT: C 994 ASP cc_start: 0.7625 (t70) cc_final: 0.7385 (t70) REVERT: C 995 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7285 (mtp180) REVERT: C 1119 ASN cc_start: 0.8233 (m-40) cc_final: 0.7785 (m-40) outliers start: 48 outliers final: 15 residues processed: 283 average time/residue: 1.1113 time to fit residues: 378.5125 Evaluate side-chains 264 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 303 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 250 optimal weight: 0.0970 chunk 164 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 255 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS A 955 ASN B 61 ASN B 954 HIS C 954 HIS C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.210099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135236 restraints weight = 25792.724| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.21 r_work: 0.3285 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26163 Z= 0.114 Angle : 0.572 11.892 35709 Z= 0.283 Chirality : 0.045 0.377 4176 Planarity : 0.004 0.036 4497 Dihedral : 5.687 59.093 4556 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.03 % Favored : 97.78 % Rotamer: Outliers : 2.20 % Allowed : 10.55 % Favored : 87.25 % 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: 0.66 (0.14), residues: 3108 helix: 2.69 (0.19), residues: 678 sheet: 0.59 (0.19), residues: 648 loop : -0.52 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 452 HIS 0.006 0.001 HIS A 954 PHE 0.017 0.001 PHE B 855 TYR 0.022 0.001 TYR A1067 ARG 0.007 0.000 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 36) link_NAG-ASN : angle 3.89413 ( 108) link_BETA1-4 : bond 0.00682 ( 21) link_BETA1-4 : angle 2.64691 ( 63) hydrogen bonds : bond 0.04300 ( 1043) hydrogen bonds : angle 5.31894 ( 2985) SS BOND : bond 0.00186 ( 39) SS BOND : angle 0.63667 ( 78) covalent geometry : bond 0.00248 (26067) covalent geometry : angle 0.51954 (35460) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1827 (OUTLIER) cc_final: 0.1281 (mttp) REVERT: A 177 MET cc_start: 0.2807 (mmm) cc_final: 0.1990 (pmm) REVERT: A 190 ARG cc_start: 0.7786 (mtt90) cc_final: 0.6851 (mtm-85) REVERT: A 382 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7774 (m) REVERT: A 514 SER cc_start: 0.7925 (m) cc_final: 0.7664 (p) REVERT: A 569 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8110 (tp) REVERT: A 646 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.7980 (mtm180) REVERT: A 821 LEU cc_start: 0.8329 (tp) cc_final: 0.8037 (mp) REVERT: A 964 LYS cc_start: 0.8602 (mmmt) cc_final: 0.7961 (mtpt) REVERT: A 994 ASP cc_start: 0.7766 (t70) cc_final: 0.7476 (t70) REVERT: A 995 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7338 (mtp180) REVERT: B 177 MET cc_start: 0.2308 (mmm) cc_final: 0.1613 (pmm) REVERT: B 190 ARG cc_start: 0.7863 (mtt90) cc_final: 0.6963 (mtm-85) REVERT: B 382 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7858 (m) REVERT: B 569 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (tp) REVERT: B 646 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.7975 (mtt90) REVERT: B 787 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8258 (mm-40) REVERT: B 821 LEU cc_start: 0.8287 (tp) cc_final: 0.8005 (mp) REVERT: B 916 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8378 (tt) REVERT: B 921 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8091 (mptt) REVERT: B 964 LYS cc_start: 0.8448 (mmmm) cc_final: 0.7822 (mtpt) REVERT: B 995 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7335 (mtp180) REVERT: B 1119 ASN cc_start: 0.8249 (m-40) cc_final: 0.7844 (m-40) REVERT: C 28 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6648 (t80) REVERT: C 77 LYS cc_start: 0.1989 (OUTLIER) cc_final: 0.1325 (mttp) REVERT: C 177 MET cc_start: 0.2598 (mmm) cc_final: 0.1947 (pmm) REVERT: C 190 ARG cc_start: 0.7874 (mtt90) cc_final: 0.6831 (mtm-85) REVERT: C 206 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8088 (tmtm) REVERT: C 269 TYR cc_start: 0.8242 (m-80) cc_final: 0.7953 (m-80) REVERT: C 382 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7843 (m) REVERT: C 514 SER cc_start: 0.7859 (m) cc_final: 0.7563 (p) REVERT: C 646 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.7865 (mtt90) REVERT: C 787 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: C 811 LYS cc_start: 0.6340 (mttp) cc_final: 0.5495 (ptpt) REVERT: C 821 LEU cc_start: 0.8282 (tp) cc_final: 0.7985 (mp) REVERT: C 921 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8293 (ttpp) REVERT: C 964 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8262 (tptm) REVERT: C 994 ASP cc_start: 0.7645 (t70) cc_final: 0.7398 (t70) REVERT: C 995 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7281 (mtp180) REVERT: C 1119 ASN cc_start: 0.8290 (m-40) cc_final: 0.7924 (m-40) outliers start: 61 outliers final: 24 residues processed: 279 average time/residue: 1.0794 time to fit residues: 361.3525 Evaluate side-chains 270 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 124 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 314 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS B 61 ASN B 954 HIS B 955 ASN C 954 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.205873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127820 restraints weight = 25531.992| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.12 r_work: 0.3203 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26163 Z= 0.180 Angle : 0.640 12.113 35709 Z= 0.317 Chirality : 0.050 0.731 4176 Planarity : 0.004 0.036 4497 Dihedral : 5.914 55.412 4556 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.38 % Favored : 97.43 % Rotamer: Outliers : 2.28 % Allowed : 10.47 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.14), residues: 3108 helix: 2.57 (0.20), residues: 657 sheet: 0.46 (0.20), residues: 627 loop : -0.57 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 452 HIS 0.006 0.001 HIS A1083 PHE 0.021 0.002 PHE B 855 TYR 0.025 0.002 TYR B1067 ARG 0.008 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.01042 ( 36) link_NAG-ASN : angle 4.19846 ( 108) link_BETA1-4 : bond 0.00736 ( 21) link_BETA1-4 : angle 2.76894 ( 63) hydrogen bonds : bond 0.05176 ( 1043) hydrogen bonds : angle 5.56870 ( 2985) SS BOND : bond 0.00316 ( 39) SS BOND : angle 0.76491 ( 78) covalent geometry : bond 0.00421 (26067) covalent geometry : angle 0.58599 (35460) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1840 (OUTLIER) cc_final: 0.1273 (mttp) REVERT: A 177 MET cc_start: 0.2781 (mmm) cc_final: 0.1997 (pmm) REVERT: A 190 ARG cc_start: 0.7791 (mtt90) cc_final: 0.6894 (mtm-85) REVERT: A 382 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7956 (m) REVERT: A 514 SER cc_start: 0.7902 (m) cc_final: 0.7644 (p) REVERT: A 646 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8077 (mtm180) REVERT: A 786 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7514 (mttp) REVERT: A 787 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8401 (mm-40) REVERT: A 821 LEU cc_start: 0.8390 (tp) cc_final: 0.8086 (mp) REVERT: A 964 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8055 (mtpt) REVERT: A 995 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7452 (mtp180) REVERT: A 1113 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 177 MET cc_start: 0.2385 (mmm) cc_final: 0.1675 (pmm) REVERT: B 190 ARG cc_start: 0.7879 (mtt90) cc_final: 0.6989 (mtm-85) REVERT: B 326 ILE cc_start: 0.7574 (mp) cc_final: 0.7346 (mp) REVERT: B 355 ARG cc_start: 0.7118 (ttt90) cc_final: 0.6522 (mmm-85) REVERT: B 382 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7986 (m) REVERT: B 569 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8060 (tp) REVERT: B 646 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8028 (mtt90) REVERT: B 787 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8348 (mm-40) REVERT: B 821 LEU cc_start: 0.8300 (tp) cc_final: 0.7958 (mp) REVERT: B 916 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 921 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8278 (ttpp) REVERT: B 964 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7947 (mtpt) REVERT: B 995 ARG cc_start: 0.8049 (mtt90) cc_final: 0.7468 (mtp180) REVERT: C 77 LYS cc_start: 0.1887 (OUTLIER) cc_final: 0.1228 (mttp) REVERT: C 177 MET cc_start: 0.2646 (mmm) cc_final: 0.1977 (pmm) REVERT: C 190 ARG cc_start: 0.7898 (mtt90) cc_final: 0.6860 (mtm-85) REVERT: C 206 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8207 (tmtm) REVERT: C 269 TYR cc_start: 0.8283 (m-80) cc_final: 0.8021 (m-80) REVERT: C 382 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7982 (m) REVERT: C 514 SER cc_start: 0.7965 (m) cc_final: 0.7656 (p) REVERT: C 646 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7928 (mtt90) REVERT: C 787 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8351 (mm-40) REVERT: C 821 LEU cc_start: 0.8382 (tp) cc_final: 0.8036 (mp) REVERT: C 921 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8314 (ttpp) REVERT: C 964 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8298 (tptm) REVERT: C 994 ASP cc_start: 0.7816 (t70) cc_final: 0.7551 (t70) REVERT: C 995 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7375 (mtp180) REVERT: C 1113 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7934 (mm-40) outliers start: 63 outliers final: 30 residues processed: 274 average time/residue: 1.1146 time to fit residues: 367.0257 Evaluate side-chains 273 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 790 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 271 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 232 optimal weight: 0.2980 chunk 94 optimal weight: 0.0980 chunk 265 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 299 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 GLN A 954 HIS B 61 ASN B 239 GLN B 954 HIS C 239 GLN C 954 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.207792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130892 restraints weight = 25692.816| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.10 r_work: 0.3247 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26163 Z= 0.125 Angle : 0.595 12.070 35709 Z= 0.294 Chirality : 0.047 0.488 4176 Planarity : 0.004 0.036 4497 Dihedral : 7.501 118.473 4556 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.09 % Favored : 97.72 % Rotamer: Outliers : 2.06 % Allowed : 11.23 % Favored : 86.71 % 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: 0.49 (0.14), residues: 3108 helix: 2.51 (0.19), residues: 675 sheet: 0.42 (0.19), residues: 639 loop : -0.57 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.007 0.001 HIS C 954 PHE 0.023 0.001 PHE B1075 TYR 0.020 0.001 TYR A1067 ARG 0.008 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 36) link_NAG-ASN : angle 4.21446 ( 108) link_BETA1-4 : bond 0.00660 ( 21) link_BETA1-4 : angle 2.58597 ( 63) hydrogen bonds : bond 0.04508 ( 1043) hydrogen bonds : angle 5.40157 ( 2985) SS BOND : bond 0.00196 ( 39) SS BOND : angle 0.64317 ( 78) covalent geometry : bond 0.00275 (26067) covalent geometry : angle 0.53827 (35460) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6810 (t80) REVERT: A 30 ASN cc_start: 0.5936 (OUTLIER) cc_final: 0.5632 (t0) REVERT: A 77 LYS cc_start: 0.1832 (OUTLIER) cc_final: 0.1263 (mttp) REVERT: A 177 MET cc_start: 0.2714 (mmm) cc_final: 0.1924 (pmm) REVERT: A 190 ARG cc_start: 0.7776 (mtt90) cc_final: 0.6849 (mtm-85) REVERT: A 382 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7888 (m) REVERT: A 514 SER cc_start: 0.7852 (m) cc_final: 0.7622 (p) REVERT: A 646 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.8040 (mtm180) REVERT: A 786 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7495 (mttp) REVERT: A 787 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8375 (mm-40) REVERT: A 821 LEU cc_start: 0.8384 (tp) cc_final: 0.8087 (mp) REVERT: A 964 LYS cc_start: 0.8615 (mmmt) cc_final: 0.7991 (mtpt) REVERT: A 995 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7409 (mtp180) REVERT: B 177 MET cc_start: 0.2420 (mmm) cc_final: 0.1696 (pmm) REVERT: B 190 ARG cc_start: 0.7836 (mtt90) cc_final: 0.6943 (mtm-85) REVERT: B 326 ILE cc_start: 0.7530 (mp) cc_final: 0.7259 (mp) REVERT: B 382 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7916 (m) REVERT: B 569 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8067 (tp) REVERT: B 646 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8014 (mtt90) REVERT: B 787 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8232 (mm-40) REVERT: B 821 LEU cc_start: 0.8301 (tp) cc_final: 0.7982 (mp) REVERT: B 916 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 921 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8281 (ttpp) REVERT: B 964 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7891 (mtpt) REVERT: B 995 ARG cc_start: 0.7989 (mtt90) cc_final: 0.7412 (mtp180) REVERT: C 77 LYS cc_start: 0.1869 (OUTLIER) cc_final: 0.1205 (mttp) REVERT: C 177 MET cc_start: 0.2661 (mmm) cc_final: 0.1982 (pmm) REVERT: C 190 ARG cc_start: 0.7869 (mtt90) cc_final: 0.6832 (mtm-85) REVERT: C 206 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8182 (tmtm) REVERT: C 382 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7881 (m) REVERT: C 514 SER cc_start: 0.7914 (m) cc_final: 0.7610 (p) REVERT: C 646 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.7920 (mtt90) REVERT: C 787 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8273 (mm-40) REVERT: C 821 LEU cc_start: 0.8349 (tp) cc_final: 0.8024 (mp) REVERT: C 921 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8291 (ttpp) REVERT: C 964 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8281 (tptm) REVERT: C 994 ASP cc_start: 0.7711 (t70) cc_final: 0.7449 (t70) REVERT: C 995 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7319 (mtp180) REVERT: C 1005 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: C 1113 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7896 (mm-40) outliers start: 57 outliers final: 25 residues processed: 275 average time/residue: 1.1230 time to fit residues: 369.2569 Evaluate side-chains 273 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 111 optimal weight: 4.9990 chunk 275 optimal weight: 0.7980 chunk 267 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 954 HIS B 61 ASN B 677 GLN B 954 HIS C 677 GLN C 954 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.206703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131283 restraints weight = 25491.500| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.06 r_work: 0.3228 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26163 Z= 0.143 Angle : 0.597 13.353 35709 Z= 0.296 Chirality : 0.047 0.497 4176 Planarity : 0.004 0.036 4497 Dihedral : 6.874 112.145 4556 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.48 % Favored : 97.33 % Rotamer: Outliers : 1.99 % Allowed : 11.34 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (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: 0.43 (0.14), residues: 3108 helix: 2.48 (0.19), residues: 675 sheet: 0.44 (0.20), residues: 624 loop : -0.63 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 452 HIS 0.006 0.001 HIS C 954 PHE 0.021 0.002 PHE B 238 TYR 0.023 0.001 TYR A1067 ARG 0.006 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 36) link_NAG-ASN : angle 3.83001 ( 108) link_BETA1-4 : bond 0.00677 ( 21) link_BETA1-4 : angle 2.49897 ( 63) hydrogen bonds : bond 0.04708 ( 1043) hydrogen bonds : angle 5.42557 ( 2985) SS BOND : bond 0.00244 ( 39) SS BOND : angle 0.68919 ( 78) covalent geometry : bond 0.00328 (26067) covalent geometry : angle 0.54923 (35460) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1876 (OUTLIER) cc_final: 0.1244 (mttp) REVERT: A 153 MET cc_start: 0.3164 (mmt) cc_final: 0.2627 (mmt) REVERT: A 177 MET cc_start: 0.2717 (mmm) cc_final: 0.1955 (pmm) REVERT: A 190 ARG cc_start: 0.7796 (mtt90) cc_final: 0.6895 (mtm-85) REVERT: A 382 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7886 (m) REVERT: A 514 SER cc_start: 0.7867 (m) cc_final: 0.7620 (p) REVERT: A 565 PHE cc_start: 0.6710 (m-10) cc_final: 0.6207 (m-10) REVERT: A 646 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8059 (mtm180) REVERT: A 787 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8401 (mm-40) REVERT: A 821 LEU cc_start: 0.8392 (tp) cc_final: 0.8077 (mp) REVERT: A 964 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8105 (mtpt) REVERT: A 995 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7391 (mtp180) REVERT: B 177 MET cc_start: 0.2455 (mmm) cc_final: 0.1753 (pmm) REVERT: B 190 ARG cc_start: 0.7848 (mtt90) cc_final: 0.6977 (mtm-85) REVERT: B 355 ARG cc_start: 0.7109 (ttt90) cc_final: 0.6386 (mmm-85) REVERT: B 382 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 569 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 646 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8022 (mtt90) REVERT: B 787 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8344 (mm-40) REVERT: B 821 LEU cc_start: 0.8303 (tp) cc_final: 0.7947 (mp) REVERT: B 916 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8494 (tt) REVERT: B 921 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8036 (mptt) REVERT: B 964 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.7907 (mtpt) REVERT: B 995 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7407 (mtp180) REVERT: C 77 LYS cc_start: 0.1848 (OUTLIER) cc_final: 0.1230 (mttp) REVERT: C 177 MET cc_start: 0.2801 (mmm) cc_final: 0.2101 (pmm) REVERT: C 190 ARG cc_start: 0.7893 (mtt90) cc_final: 0.6860 (mtm-85) REVERT: C 206 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8182 (tmtm) REVERT: C 269 TYR cc_start: 0.8324 (m-80) cc_final: 0.8101 (m-80) REVERT: C 382 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7933 (m) REVERT: C 514 SER cc_start: 0.7952 (m) cc_final: 0.7624 (p) REVERT: C 646 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.7936 (mtt90) REVERT: C 787 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8339 (mm-40) REVERT: C 821 LEU cc_start: 0.8363 (tp) cc_final: 0.8016 (mp) REVERT: C 921 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8329 (ttpp) REVERT: C 964 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8309 (tptm) REVERT: C 994 ASP cc_start: 0.7731 (t70) cc_final: 0.7457 (t70) REVERT: C 995 ARG cc_start: 0.7944 (mtt90) cc_final: 0.7341 (mtp180) REVERT: C 1005 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: C 1113 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7900 (mm-40) outliers start: 55 outliers final: 25 residues processed: 275 average time/residue: 1.1501 time to fit residues: 377.5090 Evaluate side-chains 261 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 163 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 271 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 294 optimal weight: 0.0170 chunk 307 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS A1119 ASN B 61 ASN B 954 HIS C 954 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.208062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.133110 restraints weight = 25782.194| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.98 r_work: 0.3280 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26163 Z= 0.111 Angle : 0.565 14.455 35709 Z= 0.279 Chirality : 0.047 0.619 4176 Planarity : 0.004 0.035 4497 Dihedral : 6.742 114.975 4556 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.22 % Favored : 97.59 % Rotamer: Outliers : 1.66 % Allowed : 11.81 % Favored : 86.53 % 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: 0.52 (0.14), residues: 3108 helix: 2.58 (0.19), residues: 678 sheet: 0.47 (0.19), residues: 636 loop : -0.59 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.009 0.001 HIS A 954 PHE 0.023 0.001 PHE B 238 TYR 0.020 0.001 TYR A1067 ARG 0.007 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 36) link_NAG-ASN : angle 3.84422 ( 108) link_BETA1-4 : bond 0.00633 ( 21) link_BETA1-4 : angle 2.41175 ( 63) hydrogen bonds : bond 0.04217 ( 1043) hydrogen bonds : angle 5.27730 ( 2985) SS BOND : bond 0.00183 ( 39) SS BOND : angle 0.61654 ( 78) covalent geometry : bond 0.00240 (26067) covalent geometry : angle 0.51507 (35460) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 242 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1774 (OUTLIER) cc_final: 0.1177 (mttp) REVERT: A 177 MET cc_start: 0.2819 (mmm) cc_final: 0.2007 (pmm) REVERT: A 190 ARG cc_start: 0.7799 (mtt90) cc_final: 0.6876 (mtm-85) REVERT: A 382 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7870 (m) REVERT: A 514 SER cc_start: 0.7901 (m) cc_final: 0.7657 (p) REVERT: A 565 PHE cc_start: 0.6645 (m-10) cc_final: 0.6137 (m-10) REVERT: A 646 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8012 (mtm180) REVERT: A 787 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8382 (mm-40) REVERT: A 821 LEU cc_start: 0.8381 (tp) cc_final: 0.8086 (mp) REVERT: A 964 LYS cc_start: 0.8618 (mmmt) cc_final: 0.7975 (mtpt) REVERT: A 995 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7356 (mtp180) REVERT: A 1010 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: B 77 LYS cc_start: 0.2016 (OUTLIER) cc_final: 0.1312 (mttp) REVERT: B 177 MET cc_start: 0.2483 (mmm) cc_final: 0.1779 (pmm) REVERT: B 190 ARG cc_start: 0.7844 (mtt90) cc_final: 0.6830 (mtm-85) REVERT: B 355 ARG cc_start: 0.7167 (ttt90) cc_final: 0.6534 (mmm-85) REVERT: B 382 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7899 (m) REVERT: B 569 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8105 (tp) REVERT: B 646 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.7959 (mtm180) REVERT: B 787 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8220 (mm-40) REVERT: B 821 LEU cc_start: 0.8279 (tp) cc_final: 0.7995 (mp) REVERT: B 921 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8047 (mptt) REVERT: B 964 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7850 (mtpt) REVERT: B 995 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7385 (mtp180) REVERT: B 1119 ASN cc_start: 0.8233 (m-40) cc_final: 0.8001 (m-40) REVERT: C 77 LYS cc_start: 0.1839 (OUTLIER) cc_final: 0.1193 (mttp) REVERT: C 177 MET cc_start: 0.2822 (mmm) cc_final: 0.2134 (pmm) REVERT: C 190 ARG cc_start: 0.7904 (mtt90) cc_final: 0.6849 (mtm-85) REVERT: C 206 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8126 (tmtm) REVERT: C 382 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7858 (m) REVERT: C 514 SER cc_start: 0.7980 (m) cc_final: 0.7649 (p) REVERT: C 646 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.7919 (mtt90) REVERT: C 787 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: C 821 LEU cc_start: 0.8348 (tp) cc_final: 0.8034 (mp) REVERT: C 921 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8271 (ttpp) REVERT: C 994 ASP cc_start: 0.7615 (t70) cc_final: 0.7351 (t70) REVERT: C 995 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7314 (mtp180) REVERT: C 1005 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8413 (mt0) outliers start: 46 outliers final: 24 residues processed: 270 average time/residue: 1.1524 time to fit residues: 372.0508 Evaluate side-chains 269 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 130 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 chunk 310 optimal weight: 0.1980 chunk 145 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 292 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS B 804 GLN B 954 HIS C 954 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.206765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131422 restraints weight = 25612.244| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.23 r_work: 0.3223 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26163 Z= 0.138 Angle : 0.590 13.834 35709 Z= 0.292 Chirality : 0.048 0.553 4176 Planarity : 0.004 0.036 4497 Dihedral : 6.682 113.126 4556 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.48 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 11.99 % Favored : 86.20 % 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: 0.44 (0.14), residues: 3108 helix: 2.49 (0.19), residues: 675 sheet: 0.45 (0.19), residues: 639 loop : -0.64 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 452 HIS 0.011 0.001 HIS C 954 PHE 0.025 0.001 PHE B 238 TYR 0.022 0.001 TYR A1067 ARG 0.006 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 36) link_NAG-ASN : angle 4.01250 ( 108) link_BETA1-4 : bond 0.00651 ( 21) link_BETA1-4 : angle 2.42080 ( 63) hydrogen bonds : bond 0.04583 ( 1043) hydrogen bonds : angle 5.33321 ( 2985) SS BOND : bond 0.00253 ( 39) SS BOND : angle 0.68810 ( 78) covalent geometry : bond 0.00316 (26067) covalent geometry : angle 0.53870 (35460) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1743 (OUTLIER) cc_final: 0.1167 (mttp) REVERT: A 177 MET cc_start: 0.2903 (mmm) cc_final: 0.2075 (pmm) REVERT: A 190 ARG cc_start: 0.7796 (mtt90) cc_final: 0.6843 (mtm-85) REVERT: A 382 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7893 (m) REVERT: A 514 SER cc_start: 0.7925 (m) cc_final: 0.7648 (p) REVERT: A 565 PHE cc_start: 0.6647 (m-10) cc_final: 0.6367 (m-10) REVERT: A 646 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8036 (mtm180) REVERT: A 787 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8398 (mm-40) REVERT: A 821 LEU cc_start: 0.8397 (tp) cc_final: 0.8064 (mp) REVERT: A 964 LYS cc_start: 0.8618 (mmmt) cc_final: 0.7972 (mtpt) REVERT: A 995 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7344 (mtp180) REVERT: A 1010 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: B 77 LYS cc_start: 0.1931 (OUTLIER) cc_final: 0.1264 (mttp) REVERT: B 177 MET cc_start: 0.2515 (mmm) cc_final: 0.1801 (pmm) REVERT: B 190 ARG cc_start: 0.7844 (mtt90) cc_final: 0.6814 (mtm-85) REVERT: B 326 ILE cc_start: 0.7430 (mp) cc_final: 0.7138 (mp) REVERT: B 355 ARG cc_start: 0.7120 (ttt90) cc_final: 0.6516 (mmm-85) REVERT: B 382 VAL cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (m) REVERT: B 569 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 646 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.7971 (mtm180) REVERT: B 787 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8318 (mm-40) REVERT: B 821 LEU cc_start: 0.8260 (tp) cc_final: 0.7936 (mp) REVERT: B 921 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8018 (mptt) REVERT: B 964 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7808 (mtpt) REVERT: B 995 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7380 (mtp180) REVERT: C 77 LYS cc_start: 0.1781 (OUTLIER) cc_final: 0.1145 (mttp) REVERT: C 177 MET cc_start: 0.2906 (mmm) cc_final: 0.2174 (pmm) REVERT: C 190 ARG cc_start: 0.7897 (mtt90) cc_final: 0.6798 (mtm-85) REVERT: C 206 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8129 (tmtm) REVERT: C 382 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7865 (m) REVERT: C 514 SER cc_start: 0.7894 (m) cc_final: 0.7582 (p) REVERT: C 646 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.7931 (mtt90) REVERT: C 787 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8327 (mm-40) REVERT: C 821 LEU cc_start: 0.8340 (tp) cc_final: 0.7993 (mp) REVERT: C 921 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8298 (ttpp) REVERT: C 994 ASP cc_start: 0.7687 (t70) cc_final: 0.7410 (t70) REVERT: C 995 ARG cc_start: 0.7931 (mtt90) cc_final: 0.7301 (mtp180) REVERT: C 1005 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8426 (mt0) outliers start: 50 outliers final: 27 residues processed: 262 average time/residue: 1.2509 time to fit residues: 393.3916 Evaluate side-chains 266 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 117 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 232 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 281 optimal weight: 0.0870 chunk 71 optimal weight: 0.0030 chunk 72 optimal weight: 0.6980 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 HIS B 954 HIS C 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.208838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132531 restraints weight = 25737.605| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.13 r_work: 0.3286 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26163 Z= 0.106 Angle : 0.553 13.454 35709 Z= 0.274 Chirality : 0.048 0.912 4176 Planarity : 0.004 0.035 4497 Dihedral : 6.606 112.390 4556 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.35 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 12.46 % Favored : 85.99 % 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: 0.53 (0.15), residues: 3108 helix: 2.53 (0.19), residues: 681 sheet: 0.53 (0.19), residues: 666 loop : -0.60 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.011 0.001 HIS C 954 PHE 0.022 0.001 PHE B 238 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 36) link_NAG-ASN : angle 3.66626 ( 108) link_BETA1-4 : bond 0.00617 ( 21) link_BETA1-4 : angle 2.29269 ( 63) hydrogen bonds : bond 0.04051 ( 1043) hydrogen bonds : angle 5.17664 ( 2985) SS BOND : bond 0.00177 ( 39) SS BOND : angle 0.60210 ( 78) covalent geometry : bond 0.00228 (26067) covalent geometry : angle 0.50651 (35460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26159.31 seconds wall clock time: 455 minutes 18.87 seconds (27318.87 seconds total)