Starting phenix.real_space_refine on Mon Aug 25 05:32:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elq_48159/08_2025/9elq_48159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elq_48159/08_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_48159/08_2025/9elq_48159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elq_48159/08_2025/9elq_48159.map" model { file = "/net/cci-nas-00/data/ceres_data/9elq_48159/08_2025/9elq_48159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elq_48159/08_2025/9elq_48159.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.72, per 1000 atoms: 0.22 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: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.09 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: 5.76 Time building geometry restraints manager: 2.61 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: 0.04 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: 0.000 Normalize map: mean=0, sd=1: 10.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.580 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (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 ARG 0.024 0.002 ARG C 357 TYR 0.044 0.004 TYR A 160 PHE 0.040 0.004 PHE B 371 TRP 0.065 0.007 TRP A 452 HIS 0.011 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00761 (26067) covalent geometry : angle 1.33002 (35460) SS BOND : bond 0.00616 ( 39) SS BOND : angle 1.80194 ( 78) hydrogen bonds : bond 0.13520 ( 1043) hydrogen bonds : angle 7.45585 ( 2985) link_BETA1-4 : bond 0.01059 ( 21) link_BETA1-4 : angle 4.05693 ( 63) link_NAG-ASN : bond 0.00666 ( 36) link_NAG-ASN : angle 4.29856 ( 108) *********************** 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 : 0.751 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: 0.6623 (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: 0.7834 (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: 0.7216 (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: 0.8010 (p) REVERT: B 177 MET cc_start: 0.2228 (mmm) cc_final: 0.1676 (pmm) REVERT: B 190 ARG cc_start: 0.7470 (mtt90) cc_final: 0.6583 (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: 0.7384 (p) REVERT: B 569 ILE cc_start: 0.8152 (mp) cc_final: 0.7945 (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: 0.7511 (mtt90) REVERT: B 780 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7796 (tt0) REVERT: B 821 LEU cc_start: 0.8105 (tp) cc_final: 0.7793 (mp) REVERT: B 921 LYS cc_start: 0.8568 (ttmm) cc_final: 0.8159 (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: 0.8469 (tt0) REVERT: B 1038 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8133 (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: 0.1738 (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: 0.6508 (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: 0.7536 (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: 0.7477 (mtmt) REVERT: C 994 ASP cc_start: 0.7554 (t70) cc_final: 0.7280 (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: 0.5765 time to fit residues: 284.4365 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 : 0.726 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.0050 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 overall best weight: 0.7598 ------------------------------------------------------------------------------- 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 B 115 GLN B 564 GLN C 115 GLN C 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.210351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132408 restraints weight = 25785.623| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.25 r_work: 0.3288 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26163 Z= 0.158 Angle : 0.753 16.575 35709 Z= 0.368 Chirality : 0.052 0.610 4176 Planarity : 0.005 0.052 4497 Dihedral : 8.902 67.125 4568 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.17 % Rotamer: Outliers : 2.13 % Allowed : 7.62 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3108 helix: 2.45 (0.19), residues: 687 sheet: 0.88 (0.19), residues: 630 loop : -0.26 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 357 TYR 0.023 0.002 TYR A1067 PHE 0.023 0.002 PHE B 855 TRP 0.036 0.003 TRP B 452 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00348 (26067) covalent geometry : angle 0.66819 (35460) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.05808 ( 78) hydrogen bonds : bond 0.05408 ( 1043) hydrogen bonds : angle 6.10379 ( 2985) link_BETA1-4 : bond 0.00777 ( 21) link_BETA1-4 : angle 3.42551 ( 63) link_NAG-ASN : bond 0.00847 ( 36) link_NAG-ASN : angle 5.75937 ( 108) *********************** 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 326 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 267 time to evaluate : 0.817 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: 0.7716 (m-80) cc_final: 0.7335 (m-80) REVERT: A 153 MET cc_start: 0.3018 (mmt) cc_final: 0.1466 (ttm) REVERT: A 177 MET cc_start: 0.2424 (mmm) cc_final: 0.1651 (pmm) REVERT: A 190 ARG cc_start: 0.7681 (mtt90) cc_final: 0.6732 (mtm-85) REVERT: A 514 SER cc_start: 0.7727 (m) cc_final: 0.7438 (p) REVERT: A 646 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7903 (mtt90) REVERT: A 821 LEU cc_start: 0.8333 (tp) cc_final: 0.8064 (mp) REVERT: A 964 LYS cc_start: 0.8460 (mmmt) cc_final: 0.7812 (mtpt) REVERT: A 995 ARG cc_start: 0.7913 (mtt90) cc_final: 0.7375 (mtp180) REVERT: A 1119 ASN cc_start: 0.8349 (m-40) cc_final: 0.8063 (m-40) REVERT: B 65 PHE cc_start: 0.7808 (m-80) cc_final: 0.7454 (m-80) REVERT: B 177 MET cc_start: 0.2399 (mmm) cc_final: 0.1580 (pmm) REVERT: B 190 ARG cc_start: 0.7670 (mtt90) cc_final: 0.6754 (mtm-85) REVERT: B 205 SER cc_start: 0.9040 (p) cc_final: 0.8774 (t) REVERT: B 514 SER cc_start: 0.7774 (m) cc_final: 0.7496 (p) REVERT: B 554 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7278 (tptp) REVERT: B 569 ILE cc_start: 0.8022 (mp) cc_final: 0.7767 (tp) REVERT: B 646 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.7870 (mtm180) REVERT: B 821 LEU cc_start: 0.8294 (tp) cc_final: 0.7998 (mp) REVERT: B 921 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8075 (mptt) REVERT: B 964 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7829 (mtpt) REVERT: C 177 MET cc_start: 0.2493 (mmm) cc_final: 0.1685 (pmm) REVERT: C 190 ARG cc_start: 0.7783 (mtt90) cc_final: 0.6823 (mtm-85) REVERT: C 205 SER cc_start: 0.9096 (p) cc_final: 0.8891 (t) REVERT: C 269 TYR cc_start: 0.8197 (m-80) cc_final: 0.7968 (m-80) REVERT: C 355 ARG cc_start: 0.6884 (ttt90) cc_final: 0.6050 (ttt-90) REVERT: C 514 SER cc_start: 0.7750 (m) cc_final: 0.7451 (p) REVERT: C 646 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7856 (mtt90) REVERT: C 780 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7850 (pt0) REVERT: C 821 LEU cc_start: 0.8263 (tp) cc_final: 0.7974 (mp) REVERT: C 921 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8292 (ttpp) REVERT: C 964 LYS cc_start: 0.8512 (mmmt) cc_final: 0.7866 (mtpt) REVERT: C 994 ASP cc_start: 0.7698 (t70) cc_final: 0.7458 (t70) outliers start: 59 outliers final: 19 residues processed: 304 average time/residue: 0.5379 time to fit residues: 194.7334 Evaluate side-chains 246 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 554 LYS 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 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 99 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 251 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.210966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134779 restraints weight = 25976.811| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.14 r_work: 0.3307 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26163 Z= 0.121 Angle : 0.631 12.440 35709 Z= 0.311 Chirality : 0.048 0.588 4176 Planarity : 0.004 0.033 4497 Dihedral : 6.455 53.070 4556 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 1.77 % Allowed : 9.50 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.14), residues: 3108 helix: 2.58 (0.19), residues: 696 sheet: 0.62 (0.19), residues: 633 loop : -0.35 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.001 PHE B 855 TRP 0.019 0.001 TRP B 452 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00253 (26067) covalent geometry : angle 0.56497 (35460) SS BOND : bond 0.00177 ( 39) SS BOND : angle 0.75969 ( 78) hydrogen bonds : bond 0.04577 ( 1043) hydrogen bonds : angle 5.60937 ( 2985) link_BETA1-4 : bond 0.00716 ( 21) link_BETA1-4 : angle 3.05966 ( 63) link_NAG-ASN : bond 0.00958 ( 36) link_NAG-ASN : angle 4.60190 ( 108) *********************** 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 305 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 1.170 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 153 MET cc_start: 0.3114 (mmt) cc_final: 0.1402 (ttm) REVERT: A 177 MET cc_start: 0.2584 (mmm) cc_final: 0.1871 (pmm) REVERT: A 190 ARG cc_start: 0.7731 (mtt90) cc_final: 0.6825 (mtm-85) REVERT: A 514 SER cc_start: 0.7803 (m) cc_final: 0.7555 (p) REVERT: A 646 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.7962 (mtt90) REVERT: A 821 LEU cc_start: 0.8363 (tp) cc_final: 0.8091 (mp) REVERT: A 964 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7816 (mtpt) REVERT: A 994 ASP cc_start: 0.7778 (t70) cc_final: 0.7450 (t70) REVERT: A 995 ARG cc_start: 0.7848 (mtt90) cc_final: 0.7319 (mtp180) REVERT: A 1119 ASN cc_start: 0.8329 (m-40) cc_final: 0.8019 (m-40) REVERT: B 177 MET cc_start: 0.2572 (mmm) cc_final: 0.1708 (pmm) REVERT: B 190 ARG cc_start: 0.7790 (mtt90) cc_final: 0.6884 (mtm-85) REVERT: B 514 SER cc_start: 0.7772 (m) cc_final: 0.7565 (p) REVERT: B 554 LYS cc_start: 0.7592 (tmmt) cc_final: 0.7306 (tptp) REVERT: B 646 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.7962 (mtt90) REVERT: B 821 LEU cc_start: 0.8285 (tp) cc_final: 0.8006 (mp) REVERT: B 921 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8113 (mptt) REVERT: B 964 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7832 (mtpt) REVERT: C 177 MET cc_start: 0.2600 (mmm) cc_final: 0.1868 (pmm) REVERT: C 190 ARG cc_start: 0.7869 (mtt90) cc_final: 0.6913 (mtm-85) REVERT: C 269 TYR cc_start: 0.8220 (m-80) cc_final: 0.7975 (m-80) REVERT: C 273 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7254 (mmm160) REVERT: C 355 ARG cc_start: 0.6929 (ttt90) cc_final: 0.6613 (ttt-90) REVERT: C 514 SER cc_start: 0.7875 (m) cc_final: 0.7564 (p) REVERT: C 554 LYS cc_start: 0.7397 (tmmt) cc_final: 0.7163 (tmmt) REVERT: C 646 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7869 (mtt90) REVERT: C 787 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8172 (mm-40) REVERT: C 811 LYS cc_start: 0.6321 (mttp) cc_final: 0.5557 (ptpt) REVERT: C 821 LEU cc_start: 0.8296 (tp) cc_final: 0.8026 (mp) REVERT: C 921 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8299 (ttpp) REVERT: C 964 LYS cc_start: 0.8526 (mmmt) cc_final: 0.7897 (mtpt) REVERT: C 994 ASP cc_start: 0.7659 (t70) cc_final: 0.7414 (t70) outliers start: 49 outliers final: 22 residues processed: 288 average time/residue: 0.5336 time to fit residues: 183.8808 Evaluate side-chains 252 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 967 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 27 SER 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 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 273 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 184 optimal weight: 0.4980 chunk 240 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 308 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 955 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.206402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128768 restraints weight = 25565.698| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.09 r_work: 0.3214 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26163 Z= 0.171 Angle : 0.640 11.995 35709 Z= 0.321 Chirality : 0.048 0.296 4176 Planarity : 0.004 0.035 4497 Dihedral : 6.067 58.086 4556 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.19 % Favored : 97.62 % Rotamer: Outliers : 2.74 % Allowed : 9.14 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3108 helix: 2.34 (0.19), residues: 693 sheet: 0.48 (0.19), residues: 657 loop : -0.53 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 355 TYR 0.026 0.002 TYR B1067 PHE 0.020 0.002 PHE B 855 TRP 0.012 0.002 TRP B 452 HIS 0.006 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00396 (26067) covalent geometry : angle 0.58580 (35460) SS BOND : bond 0.00290 ( 39) SS BOND : angle 0.81274 ( 78) hydrogen bonds : bond 0.05218 ( 1043) hydrogen bonds : angle 5.67424 ( 2985) link_BETA1-4 : bond 0.00768 ( 21) link_BETA1-4 : angle 2.99037 ( 63) link_NAG-ASN : bond 0.01022 ( 36) link_NAG-ASN : angle 4.12689 ( 108) *********************** 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 323 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 247 time to evaluate : 0.931 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: 0.1742 (OUTLIER) cc_final: 0.1213 (mttp) REVERT: A 177 MET cc_start: 0.2816 (mmm) cc_final: 0.1986 (pmm) REVERT: A 190 ARG cc_start: 0.7791 (mtt90) cc_final: 0.6891 (mtm-85) REVERT: A 382 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7969 (m) REVERT: A 514 SER cc_start: 0.7909 (m) cc_final: 0.7619 (p) REVERT: A 569 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 646 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8078 (mtm180) REVERT: A 787 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8351 (mm-40) REVERT: A 821 LEU cc_start: 0.8410 (tp) cc_final: 0.8120 (mp) REVERT: A 964 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8053 (mtpt) REVERT: A 995 ARG cc_start: 0.8008 (mtt90) cc_final: 0.7470 (mtp180) REVERT: A 1113 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: B 177 MET cc_start: 0.2281 (mmm) cc_final: 0.1527 (pmm) REVERT: B 190 ARG cc_start: 0.7896 (mtt90) cc_final: 0.7020 (mtm-85) REVERT: B 382 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7995 (m) REVERT: B 514 SER cc_start: 0.7853 (m) cc_final: 0.7650 (p) REVERT: B 569 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8059 (tp) REVERT: B 646 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8033 (mtt90) REVERT: B 787 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8336 (mm-40) REVERT: B 821 LEU cc_start: 0.8305 (tp) cc_final: 0.7988 (mp) REVERT: B 916 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8495 (tt) REVERT: B 921 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8285 (ttpp) REVERT: B 964 LYS cc_start: 0.8531 (mmmm) cc_final: 0.7943 (mtpt) REVERT: B 1038 LYS cc_start: 0.8764 (mttp) cc_final: 0.8210 (mmtp) REVERT: C 77 LYS cc_start: 0.1951 (OUTLIER) cc_final: 0.1357 (mttp) REVERT: C 177 MET cc_start: 0.2650 (mmm) cc_final: 0.1970 (pmm) REVERT: C 190 ARG cc_start: 0.7917 (mtt90) cc_final: 0.6928 (mtm-85) REVERT: C 206 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8227 (tmtm) REVERT: C 269 TYR cc_start: 0.8262 (m-80) cc_final: 0.8061 (m-80) REVERT: C 355 ARG cc_start: 0.6871 (ttt90) cc_final: 0.6257 (ttt-90) REVERT: C 382 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.8009 (m) REVERT: C 514 SER cc_start: 0.7909 (m) cc_final: 0.7595 (p) REVERT: C 646 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.7949 (mtt90) REVERT: C 787 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: C 821 LEU cc_start: 0.8360 (tp) cc_final: 0.8045 (mp) REVERT: C 921 LYS cc_start: 0.8721 (ttmm) cc_final: 0.8342 (ttpp) REVERT: C 964 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8047 (mtpt) REVERT: C 994 ASP cc_start: 0.7825 (t70) cc_final: 0.7570 (t70) REVERT: C 995 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7369 (mtp180) REVERT: C 1113 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7909 (mm-40) outliers start: 76 outliers final: 33 residues processed: 285 average time/residue: 0.5088 time to fit residues: 172.9025 Evaluate side-chains 275 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 572 THR 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 900 MET 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 27 SER 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 549 THR 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 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 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 549 THR 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 902 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 209 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 310 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 613 GLN B 61 ASN B 613 GLN B1142 GLN C 87 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.203556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127215 restraints weight = 25418.413| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.10 r_work: 0.3148 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26163 Z= 0.229 Angle : 0.714 20.555 35709 Z= 0.353 Chirality : 0.053 0.785 4176 Planarity : 0.005 0.040 4497 Dihedral : 6.352 56.453 4556 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 2.42 % Allowed : 10.22 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.14), residues: 3108 helix: 2.15 (0.20), residues: 675 sheet: 0.52 (0.20), residues: 615 loop : -0.72 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 815 TYR 0.025 0.002 TYR B1067 PHE 0.028 0.002 PHE A1075 TRP 0.012 0.002 TRP C 452 HIS 0.008 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00546 (26067) covalent geometry : angle 0.65247 (35460) SS BOND : bond 0.00418 ( 39) SS BOND : angle 0.86702 ( 78) hydrogen bonds : bond 0.05709 ( 1043) hydrogen bonds : angle 5.81582 ( 2985) link_BETA1-4 : bond 0.00748 ( 21) link_BETA1-4 : angle 3.00765 ( 63) link_NAG-ASN : bond 0.00770 ( 36) link_NAG-ASN : angle 4.76874 ( 108) *********************** 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 310 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1852 (OUTLIER) cc_final: 0.1271 (mttp) REVERT: A 177 MET cc_start: 0.2687 (mmm) cc_final: 0.1892 (pmm) REVERT: A 190 ARG cc_start: 0.7814 (mtt90) cc_final: 0.6867 (mtm-85) REVERT: A 514 SER cc_start: 0.7888 (m) cc_final: 0.7611 (p) REVERT: A 554 LYS cc_start: 0.7647 (tmmt) cc_final: 0.7425 (tmmt) REVERT: A 565 PHE cc_start: 0.6790 (m-10) cc_final: 0.6267 (m-10) REVERT: A 646 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8066 (mtm180) REVERT: A 787 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8421 (mm-40) REVERT: A 821 LEU cc_start: 0.8435 (tp) cc_final: 0.8124 (mp) REVERT: A 964 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8137 (mtpt) REVERT: A 995 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7517 (mtp180) REVERT: A 1113 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: A 1119 ASN cc_start: 0.8730 (m-40) cc_final: 0.8478 (m110) REVERT: B 77 LYS cc_start: 0.1963 (OUTLIER) cc_final: 0.1260 (mttp) REVERT: B 177 MET cc_start: 0.2658 (mmm) cc_final: 0.1833 (pmm) REVERT: B 190 ARG cc_start: 0.7872 (mtt90) cc_final: 0.6991 (mtm-85) REVERT: B 355 ARG cc_start: 0.6957 (ttt90) cc_final: 0.6556 (ttt90) REVERT: B 569 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 646 ARG cc_start: 0.8545 (mmm-85) cc_final: 0.8045 (mtm180) REVERT: B 916 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 921 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8289 (ttpp) REVERT: B 964 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7957 (mtpt) REVERT: B 995 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7490 (mtp180) REVERT: B 1050 MET cc_start: 0.9274 (ptm) cc_final: 0.9046 (ptm) REVERT: B 1119 ASN cc_start: 0.8639 (m-40) cc_final: 0.8400 (m110) REVERT: C 177 MET cc_start: 0.2926 (mmm) cc_final: 0.2170 (pmm) REVERT: C 190 ARG cc_start: 0.7869 (mtt90) cc_final: 0.6837 (mtm-85) REVERT: C 206 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8288 (tmtm) REVERT: C 269 TYR cc_start: 0.8344 (m-80) cc_final: 0.8108 (m-80) REVERT: C 355 ARG cc_start: 0.6839 (ttt90) cc_final: 0.6243 (ttt-90) REVERT: C 382 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8112 (m) REVERT: C 514 SER cc_start: 0.7952 (m) cc_final: 0.7606 (p) REVERT: C 646 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.7929 (mtt90) REVERT: C 787 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: C 821 LEU cc_start: 0.8394 (tp) cc_final: 0.8018 (mp) REVERT: C 921 LYS cc_start: 0.8763 (ttmm) cc_final: 0.8368 (ttpp) REVERT: C 964 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8080 (mtpt) REVERT: C 995 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7389 (mtp180) REVERT: C 1005 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8410 (mt0) REVERT: C 1010 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8413 (mp10) outliers start: 67 outliers final: 33 residues processed: 278 average time/residue: 0.5535 time to fit residues: 181.1382 Evaluate side-chains 265 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 LYS 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 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 878 LEU Chi-restraints excluded: chain A residue 900 MET 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 77 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 549 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 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 206 LYS 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 534 VAL Chi-restraints excluded: chain C residue 549 THR 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 902 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1010 GLN 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 260 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 275 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 677 GLN A 954 HIS B 61 ASN B 99 ASN B 115 GLN B 321 GLN B 677 GLN B 954 HIS C 115 GLN C 677 GLN C 804 GLN C 954 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.203647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.126638 restraints weight = 25521.740| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.03 r_work: 0.3162 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26163 Z= 0.211 Angle : 0.684 15.250 35709 Z= 0.338 Chirality : 0.050 0.506 4176 Planarity : 0.004 0.038 4497 Dihedral : 7.242 115.548 4556 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.30 % Rotamer: Outliers : 2.31 % Allowed : 11.34 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3108 helix: 2.15 (0.20), residues: 675 sheet: 0.43 (0.20), residues: 639 loop : -0.83 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.023 0.002 TYR A1067 PHE 0.027 0.002 PHE C 855 TRP 0.014 0.002 TRP B 633 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00503 (26067) covalent geometry : angle 0.62505 (35460) SS BOND : bond 0.00375 ( 39) SS BOND : angle 0.82983 ( 78) hydrogen bonds : bond 0.05477 ( 1043) hydrogen bonds : angle 5.76994 ( 2985) link_BETA1-4 : bond 0.00711 ( 21) link_BETA1-4 : angle 2.88461 ( 63) link_NAG-ASN : bond 0.00889 ( 36) link_NAG-ASN : angle 4.57699 ( 108) *********************** 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 292 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.961 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 28 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.7087 (t80) REVERT: A 77 LYS cc_start: 0.1948 (OUTLIER) cc_final: 0.1289 (mttp) REVERT: A 177 MET cc_start: 0.2813 (mmm) cc_final: 0.1910 (pmm) REVERT: A 190 ARG cc_start: 0.7818 (mtt90) cc_final: 0.6906 (mtm-85) REVERT: A 514 SER cc_start: 0.7951 (m) cc_final: 0.7654 (p) REVERT: A 554 LYS cc_start: 0.7660 (tmmt) cc_final: 0.7451 (tmmt) REVERT: A 565 PHE cc_start: 0.6745 (m-10) cc_final: 0.6385 (m-10) REVERT: A 646 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8095 (mtm180) REVERT: A 787 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (mm-40) REVERT: A 821 LEU cc_start: 0.8438 (tp) cc_final: 0.8128 (mp) REVERT: A 964 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8119 (mtpt) REVERT: A 995 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7506 (mtp180) REVERT: A 1113 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8311 (mt0) REVERT: A 1119 ASN cc_start: 0.8683 (m-40) cc_final: 0.8414 (m110) REVERT: B 77 LYS cc_start: 0.1940 (OUTLIER) cc_final: 0.1215 (mttp) REVERT: B 177 MET cc_start: 0.2625 (mmm) cc_final: 0.1800 (pmm) REVERT: B 190 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7026 (mtm-85) REVERT: B 569 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8099 (tp) REVERT: B 646 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8071 (mtm180) REVERT: B 786 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7555 (mttp) REVERT: B 916 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8547 (tt) REVERT: B 921 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8302 (ttpp) REVERT: B 964 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7951 (mtpt) REVERT: B 995 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7498 (mtp180) REVERT: B 1119 ASN cc_start: 0.8628 (m-40) cc_final: 0.8374 (m110) REVERT: C 28 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6768 (t80) REVERT: C 77 LYS cc_start: 0.1822 (OUTLIER) cc_final: 0.1190 (mttp) REVERT: C 177 MET cc_start: 0.2984 (mmm) cc_final: 0.2198 (pmm) REVERT: C 190 ARG cc_start: 0.7885 (mtt90) cc_final: 0.6865 (mtm-85) REVERT: C 206 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8281 (tmtm) REVERT: C 269 TYR cc_start: 0.8375 (m-80) cc_final: 0.8164 (m-80) REVERT: C 355 ARG cc_start: 0.6825 (ttt90) cc_final: 0.6251 (ttt-90) REVERT: C 514 SER cc_start: 0.7992 (m) cc_final: 0.7632 (p) REVERT: C 646 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.7971 (mtt90) REVERT: C 787 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: C 821 LEU cc_start: 0.8390 (tp) cc_final: 0.8044 (mp) REVERT: C 921 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8377 (ttpp) REVERT: C 964 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8068 (mtpt) REVERT: C 995 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7390 (mtp180) REVERT: C 1010 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8419 (mp10) outliers start: 64 outliers final: 37 residues processed: 265 average time/residue: 0.5827 time to fit residues: 180.5514 Evaluate side-chains 270 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 LYS 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 562 PHE 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 900 MET 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 77 LYS Chi-restraints excluded: chain B residue 94 SER 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 549 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 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 28 TYR Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 VAL 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 560 LEU Chi-restraints excluded: chain C residue 562 PHE 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 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 21 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 205 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 954 HIS B 61 ASN B 115 GLN B 954 HIS C 115 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 = 0.4215 r_free = 0.4215 target = 0.205410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130840 restraints weight = 25519.414| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.20 r_work: 0.3208 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3175 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= 0.135 Angle : 0.610 13.650 35709 Z= 0.302 Chirality : 0.047 0.519 4176 Planarity : 0.004 0.051 4497 Dihedral : 6.713 113.773 4556 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 2.24 % Allowed : 11.20 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.14), residues: 3108 helix: 2.38 (0.20), residues: 675 sheet: 0.42 (0.20), residues: 609 loop : -0.78 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 355 TYR 0.020 0.001 TYR A1067 PHE 0.020 0.001 PHE C 855 TRP 0.015 0.001 TRP B 633 HIS 0.006 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00304 (26067) covalent geometry : angle 0.55597 (35460) SS BOND : bond 0.00232 ( 39) SS BOND : angle 0.67775 ( 78) hydrogen bonds : bond 0.04698 ( 1043) hydrogen bonds : angle 5.59326 ( 2985) link_BETA1-4 : bond 0.00640 ( 21) link_BETA1-4 : angle 2.62027 ( 63) link_NAG-ASN : bond 0.00710 ( 36) link_NAG-ASN : angle 4.13233 ( 108) *********************** 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 297 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 0.664 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: symmetry clash REVERT: A 77 LYS cc_start: 0.1961 (OUTLIER) cc_final: 0.1317 (mttp) REVERT: A 177 MET cc_start: 0.2853 (mmm) cc_final: 0.1982 (pmm) REVERT: A 190 ARG cc_start: 0.7780 (mtt90) cc_final: 0.6846 (mtm-85) REVERT: A 514 SER cc_start: 0.7938 (m) cc_final: 0.7643 (p) REVERT: A 565 PHE cc_start: 0.6659 (m-10) cc_final: 0.6287 (m-10) REVERT: A 646 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8050 (mtm180) REVERT: A 787 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: A 821 LEU cc_start: 0.8391 (tp) cc_final: 0.8073 (mp) REVERT: A 964 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8054 (mtpt) REVERT: A 995 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7394 (mtp180) REVERT: A 1119 ASN cc_start: 0.8572 (m-40) cc_final: 0.8274 (m110) REVERT: B 77 LYS cc_start: 0.2053 (OUTLIER) cc_final: 0.1340 (mttp) REVERT: B 177 MET cc_start: 0.2630 (mmm) cc_final: 0.1802 (pmm) REVERT: B 190 ARG cc_start: 0.7850 (mtt90) cc_final: 0.6979 (mtm-85) REVERT: B 355 ARG cc_start: 0.7176 (ttt90) cc_final: 0.6557 (mmm-85) REVERT: B 514 SER cc_start: 0.8024 (m) cc_final: 0.7724 (p) REVERT: B 569 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 646 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.7956 (mtm180) REVERT: B 821 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 916 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8472 (tt) REVERT: B 921 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8031 (mptt) REVERT: B 964 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: B 995 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7449 (mtp180) REVERT: B 1119 ASN cc_start: 0.8449 (m-40) cc_final: 0.8174 (m110) REVERT: C 77 LYS cc_start: 0.1808 (OUTLIER) cc_final: 0.1222 (mttp) REVERT: C 177 MET cc_start: 0.3198 (mmm) cc_final: 0.2362 (pmm) REVERT: C 190 ARG cc_start: 0.7861 (mtt90) cc_final: 0.6810 (mtm-85) REVERT: C 206 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8236 (tmtm) REVERT: C 269 TYR cc_start: 0.8328 (m-80) cc_final: 0.8087 (m-80) REVERT: C 355 ARG cc_start: 0.6785 (ttt90) cc_final: 0.6236 (ttt-90) REVERT: C 514 SER cc_start: 0.7922 (m) cc_final: 0.7571 (p) REVERT: C 646 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7941 (mtm180) REVERT: C 787 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: C 821 LEU cc_start: 0.8366 (tp) cc_final: 0.8032 (mp) REVERT: C 921 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8329 (ttpp) REVERT: C 964 LYS cc_start: 0.8641 (mmmt) cc_final: 0.7983 (mtpt) REVERT: C 995 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7350 (mtp180) REVERT: C 1005 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (mt0) outliers start: 62 outliers final: 25 residues processed: 276 average time/residue: 0.6059 time to fit residues: 195.3053 Evaluate side-chains 244 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 1100 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1074 ASN 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 335 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 562 PHE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 38 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 299 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN B 321 GLN B 954 HIS C 115 GLN C 954 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.205297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126451 restraints weight = 25500.896| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.06 r_work: 0.3219 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26163 Z= 0.142 Angle : 0.604 12.867 35709 Z= 0.299 Chirality : 0.047 0.565 4176 Planarity : 0.004 0.043 4497 Dihedral : 6.499 111.959 4556 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.54 % Favored : 97.27 % Rotamer: Outliers : 1.84 % Allowed : 11.81 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.14), residues: 3108 helix: 2.41 (0.20), residues: 675 sheet: 0.33 (0.19), residues: 654 loop : -0.80 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 355 TYR 0.022 0.001 TYR A1067 PHE 0.024 0.002 PHE B 238 TRP 0.014 0.001 TRP B 633 HIS 0.007 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00326 (26067) covalent geometry : angle 0.55234 (35460) SS BOND : bond 0.00259 ( 39) SS BOND : angle 0.69181 ( 78) hydrogen bonds : bond 0.04730 ( 1043) hydrogen bonds : angle 5.55942 ( 2985) link_BETA1-4 : bond 0.00675 ( 21) link_BETA1-4 : angle 2.54711 ( 63) link_NAG-ASN : bond 0.00732 ( 36) link_NAG-ASN : angle 4.04840 ( 108) *********************** 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 282 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 1.069 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: 0.1866 (OUTLIER) cc_final: 0.1202 (mttp) REVERT: A 177 MET cc_start: 0.2872 (mmm) cc_final: 0.2035 (pmm) REVERT: A 190 ARG cc_start: 0.7783 (mtt90) cc_final: 0.6855 (mtm-85) REVERT: A 514 SER cc_start: 0.7921 (m) cc_final: 0.7573 (p) REVERT: A 565 PHE cc_start: 0.6643 (m-10) cc_final: 0.6275 (m-10) REVERT: A 646 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8067 (mtm180) REVERT: A 787 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8268 (mm-40) REVERT: A 821 LEU cc_start: 0.8365 (tp) cc_final: 0.8067 (mp) REVERT: A 947 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8336 (mtmt) REVERT: A 964 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8064 (mtpt) REVERT: A 995 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7433 (mtp180) REVERT: A 1119 ASN cc_start: 0.8563 (m-40) cc_final: 0.8281 (m110) REVERT: B 77 LYS cc_start: 0.1973 (OUTLIER) cc_final: 0.1271 (mttp) REVERT: B 177 MET cc_start: 0.2690 (mmm) cc_final: 0.1860 (pmm) REVERT: B 190 ARG cc_start: 0.7816 (mtt90) cc_final: 0.6864 (mtm-85) REVERT: B 321 GLN cc_start: 0.8311 (mm110) cc_final: 0.8063 (mm-40) REVERT: B 355 ARG cc_start: 0.7042 (ttt90) cc_final: 0.6523 (mmm-85) REVERT: B 514 SER cc_start: 0.8014 (m) cc_final: 0.7654 (p) REVERT: B 569 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 646 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.7954 (mtm180) REVERT: B 821 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 916 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 921 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8049 (mptt) REVERT: B 964 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: B 995 ARG cc_start: 0.8039 (mtt90) cc_final: 0.7454 (mtp180) REVERT: B 1119 ASN cc_start: 0.8425 (m-40) cc_final: 0.8184 (m110) REVERT: C 77 LYS cc_start: 0.1738 (OUTLIER) cc_final: 0.1147 (mttp) REVERT: C 177 MET cc_start: 0.3209 (mmm) cc_final: 0.2445 (pmm) REVERT: C 190 ARG cc_start: 0.7848 (mtt90) cc_final: 0.6807 (mtm-85) REVERT: C 206 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8228 (tmtm) REVERT: C 269 TYR cc_start: 0.8286 (m-80) cc_final: 0.8056 (m-80) REVERT: C 514 SER cc_start: 0.7923 (m) cc_final: 0.7560 (p) REVERT: C 646 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.7963 (mtm180) REVERT: C 787 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: C 821 LEU cc_start: 0.8372 (tp) cc_final: 0.8062 (mp) REVERT: C 921 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8335 (ttpp) REVERT: C 964 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8002 (mtpt) REVERT: C 995 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7397 (mtp180) REVERT: C 1005 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8383 (mt0) outliers start: 51 outliers final: 29 residues processed: 265 average time/residue: 0.5944 time to fit residues: 186.1954 Evaluate side-chains 257 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 94 SER 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 1100 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 77 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 562 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 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 94 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 562 PHE 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 1005 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 159 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 282 optimal weight: 0.4980 chunk 226 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 954 HIS B 61 ASN B 613 GLN B 954 HIS C 954 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.206726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128946 restraints weight = 25650.264| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.10 r_work: 0.3263 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26163 Z= 0.115 Angle : 0.575 15.094 35709 Z= 0.285 Chirality : 0.047 0.644 4176 Planarity : 0.004 0.036 4497 Dihedral : 6.970 123.243 4556 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.38 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 12.03 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.14), residues: 3108 helix: 2.46 (0.19), residues: 681 sheet: 0.35 (0.20), residues: 624 loop : -0.71 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.021 0.001 TYR B 904 PHE 0.020 0.001 PHE B 238 TRP 0.013 0.001 TRP C 633 HIS 0.008 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00251 (26067) covalent geometry : angle 0.52504 (35460) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.62902 ( 78) hydrogen bonds : bond 0.04298 ( 1043) hydrogen bonds : angle 5.41934 ( 2985) link_BETA1-4 : bond 0.00618 ( 21) link_BETA1-4 : angle 2.40100 ( 63) link_NAG-ASN : bond 0.00728 ( 36) link_NAG-ASN : angle 3.91579 ( 108) *********************** 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 286 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1792 (OUTLIER) cc_final: 0.1176 (mttp) REVERT: A 177 MET cc_start: 0.2899 (mmm) cc_final: 0.2042 (pmm) REVERT: A 190 ARG cc_start: 0.7770 (mtt90) cc_final: 0.6830 (mtm-85) REVERT: A 514 SER cc_start: 0.7897 (m) cc_final: 0.7541 (p) REVERT: A 565 PHE cc_start: 0.6650 (m-10) cc_final: 0.6340 (m-10) REVERT: A 646 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8034 (mtm180) REVERT: A 787 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8206 (mm-40) REVERT: A 821 LEU cc_start: 0.8352 (tp) cc_final: 0.8063 (mp) REVERT: A 947 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8330 (mtmt) REVERT: A 964 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8045 (mtpt) REVERT: A 995 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7409 (mtp180) REVERT: B 77 LYS cc_start: 0.1923 (OUTLIER) cc_final: 0.1226 (mttp) REVERT: B 177 MET cc_start: 0.2656 (mmm) cc_final: 0.1830 (pmm) REVERT: B 190 ARG cc_start: 0.7822 (mtt90) cc_final: 0.6834 (mtm-85) REVERT: B 273 ARG cc_start: 0.7286 (mmt90) cc_final: 0.7038 (mmt90) REVERT: B 355 ARG cc_start: 0.7018 (ttt90) cc_final: 0.6581 (mmm-85) REVERT: B 514 SER cc_start: 0.7996 (m) cc_final: 0.7634 (p) REVERT: B 569 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8149 (tp) REVERT: B 646 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.7967 (mtm180) REVERT: B 821 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8006 (mp) REVERT: B 921 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8052 (mptt) REVERT: B 964 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7860 (mtpt) REVERT: B 995 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7405 (mtp180) REVERT: C 77 LYS cc_start: 0.1725 (OUTLIER) cc_final: 0.1158 (mttp) REVERT: C 177 MET cc_start: 0.3181 (mmm) cc_final: 0.2444 (pmm) REVERT: C 190 ARG cc_start: 0.7859 (mtt90) cc_final: 0.6829 (mtm-85) REVERT: C 206 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8155 (tmtm) REVERT: C 269 TYR cc_start: 0.8293 (m-80) cc_final: 0.8023 (m-80) REVERT: C 514 SER cc_start: 0.7965 (m) cc_final: 0.7601 (p) REVERT: C 646 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.7957 (mtm180) REVERT: C 787 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8237 (mm-40) REVERT: C 821 LEU cc_start: 0.8328 (tp) cc_final: 0.8043 (mp) REVERT: C 921 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8316 (ttpp) REVERT: C 964 LYS cc_start: 0.8638 (mmmt) cc_final: 0.7977 (mtpt) REVERT: C 995 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7355 (mtp180) REVERT: C 1005 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8352 (mt0) outliers start: 48 outliers final: 28 residues processed: 270 average time/residue: 0.5996 time to fit residues: 191.3319 Evaluate side-chains 261 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 94 SER 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 754 LEU Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 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 335 LEU 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 562 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 821 LEU 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 94 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 208 THR 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 562 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 613 GLN A 954 HIS B 87 ASN B 115 GLN B 613 GLN B 690 GLN B 954 HIS C 613 GLN C 935 GLN C 954 HIS C1119 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.202836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124879 restraints weight = 25478.656| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.12 r_work: 0.3168 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26163 Z= 0.251 Angle : 0.706 16.393 35709 Z= 0.351 Chirality : 0.054 0.919 4176 Planarity : 0.005 0.036 4497 Dihedral : 7.439 123.865 4556 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.01 % Rotamer: Outliers : 1.84 % Allowed : 12.28 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.14), residues: 3108 helix: 2.26 (0.20), residues: 657 sheet: 0.28 (0.20), residues: 648 loop : -0.88 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.032 0.002 TYR B 904 PHE 0.032 0.002 PHE B 855 TRP 0.010 0.002 TRP C 452 HIS 0.009 0.002 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00605 (26067) covalent geometry : angle 0.65356 (35460) SS BOND : bond 0.00541 ( 39) SS BOND : angle 1.36221 ( 78) hydrogen bonds : bond 0.05718 ( 1043) hydrogen bonds : angle 5.75744 ( 2985) link_BETA1-4 : bond 0.00678 ( 21) link_BETA1-4 : angle 2.68093 ( 63) link_NAG-ASN : bond 0.00807 ( 36) link_NAG-ASN : angle 4.34744 ( 108) ********************** 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 271 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.1836 (OUTLIER) cc_final: 0.0863 (ttpt) REVERT: A 177 MET cc_start: 0.3018 (mmm) cc_final: 0.2172 (pmm) REVERT: A 190 ARG cc_start: 0.7828 (mtt90) cc_final: 0.6881 (mtm-85) REVERT: A 355 ARG cc_start: 0.7184 (ttt90) cc_final: 0.6363 (mmm-85) REVERT: A 514 SER cc_start: 0.7992 (m) cc_final: 0.7594 (p) REVERT: A 565 PHE cc_start: 0.6724 (m-10) cc_final: 0.6507 (m-10) REVERT: A 646 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8128 (mtm180) REVERT: A 787 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8398 (mm-40) REVERT: A 821 LEU cc_start: 0.8467 (tp) cc_final: 0.8179 (mp) REVERT: A 947 LYS cc_start: 0.8876 (mtpp) cc_final: 0.8367 (mtmt) REVERT: A 964 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8115 (mtpt) REVERT: A 995 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7533 (mtp180) REVERT: B 77 LYS cc_start: 0.1950 (OUTLIER) cc_final: 0.1240 (mttp) REVERT: B 177 MET cc_start: 0.2813 (mmm) cc_final: 0.1955 (pmm) REVERT: B 190 ARG cc_start: 0.7835 (mtt90) cc_final: 0.6854 (mtm-85) REVERT: B 355 ARG cc_start: 0.7088 (ttt90) cc_final: 0.6577 (mmm-85) REVERT: B 529 LYS cc_start: 0.7232 (mmmt) cc_final: 0.6944 (mmtp) REVERT: B 569 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8224 (tp) REVERT: B 646 ARG cc_start: 0.8564 (mmm-85) cc_final: 0.8048 (mtm180) REVERT: B 921 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8312 (ttpp) REVERT: B 964 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7915 (mtpt) REVERT: B 995 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7519 (mtp180) REVERT: B 1119 ASN cc_start: 0.8681 (m-40) cc_final: 0.8433 (m110) REVERT: C 77 LYS cc_start: 0.1761 (OUTLIER) cc_final: 0.1162 (mttp) REVERT: C 177 MET cc_start: 0.3214 (mmm) cc_final: 0.2380 (pmm) REVERT: C 190 ARG cc_start: 0.7867 (mtt90) cc_final: 0.6845 (mtm-85) REVERT: C 206 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8294 (tmtm) REVERT: C 269 TYR cc_start: 0.8395 (m-80) cc_final: 0.8152 (m-80) REVERT: C 646 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8036 (mtm180) REVERT: C 787 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: C 821 LEU cc_start: 0.8423 (tp) cc_final: 0.8060 (mp) REVERT: C 921 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8376 (ttpp) REVERT: C 964 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8079 (mtpt) REVERT: C 995 ARG cc_start: 0.8103 (mtt90) cc_final: 0.7471 (mtp180) REVERT: C 1005 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8392 (mt0) outliers start: 51 outliers final: 34 residues processed: 255 average time/residue: 0.6332 time to fit residues: 189.5756 Evaluate side-chains 260 residues out of total 2769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 94 SER 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 754 LEU Chi-restraints excluded: chain A residue 787 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 94 SER Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 335 LEU 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 562 PHE Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 821 LEU 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 84 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 424 LYS 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 562 PHE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1005 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 129 optimal weight: 0.5980 chunk 217 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 222 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 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 115 GLN B 115 GLN B 954 HIS C 613 GLN C 954 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.203719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128548 restraints weight = 25408.964| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.23 r_work: 0.3172 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26163 Z= 0.179 Angle : 0.644 15.701 35709 Z= 0.320 Chirality : 0.050 0.817 4176 Planarity : 0.004 0.036 4497 Dihedral : 7.354 122.597 4556 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.67 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 12.57 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3108 helix: 2.30 (0.20), residues: 657 sheet: 0.26 (0.19), residues: 648 loop : -0.88 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 355 TYR 0.030 0.002 TYR B 904 PHE 0.028 0.002 PHE B 238 TRP 0.012 0.002 TRP C 353 HIS 0.011 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00424 (26067) covalent geometry : angle 0.58940 (35460) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.31277 ( 78) hydrogen bonds : bond 0.05104 ( 1043) hydrogen bonds : angle 5.66335 ( 2985) link_BETA1-4 : bond 0.00616 ( 21) link_BETA1-4 : angle 2.57179 ( 63) link_NAG-ASN : bond 0.00744 ( 36) link_NAG-ASN : angle 4.24467 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12335.22 seconds wall clock time: 210 minutes 11.92 seconds (12611.92 seconds total)