Starting phenix.real_space_refine on Sun Jun 22 07:46:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.cif Found real_map, /net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.map" model { file = "/net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9elh_48149/06_2025/9elh_48149.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 110 5.16 5 C 16283 2.51 5 N 4148 2.21 5 O 4971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25512 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8286 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 56, 'TRANS': 999} Chain breaks: 6 Chain: "B" Number of atoms: 8173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8173 Classifications: {'peptide': 1045} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 54, 'TRANS': 990} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 8248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8248 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 56, 'TRANS': 994} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: "F" 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: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: 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: "Q" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 20.99, per 1000 atoms: 0.82 Number of scatterers: 25512 At special positions: 0 Unit cell: (129.958, 129.24, 201.04, 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 110 16.00 O 4971 8.00 N 4148 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=1.69 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=1.55 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.87 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 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=2.05 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 Atom "HETATM25314 O5 NAG A1310 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 354 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 30 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 30 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 165 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 709 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 354 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 30 " " NAG D 1 " - " ASN A1134 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN B 709 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN B 282 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C 717 " Time building additional restraints: 7.58 Conformation dependent library (CDL) restraints added in 3.4 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 40 sheets defined 27.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.572A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.769A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.354A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 737 through 744 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 removed outlier: 3.607A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 827 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 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.296A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (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: 3.948A 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: 4.313A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.949A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.426A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) 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 744 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: 4.269A 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 945 through 965 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: 4.198A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1149 removed outlier: 3.657A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.877A pdb=" N GLY C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.661A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.680A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.715A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 removed outlier: 4.135A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.908A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA C 411 " --> pdb=" O SER C 408 " (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 502 through 505 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 891 removed outlier: 4.289A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.952A 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 945 through 965 removed outlier: 3.942A 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: 3.901A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1149 removed outlier: 3.908A pdb=" N SER C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.109A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.128A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.892A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.865A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.268A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.055A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.785A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.678A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.503A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.637A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 4.144A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.934A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 29 removed outlier: 5.751A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.636A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC3, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.491A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.193A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.533A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.694A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.545A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 28 removed outlier: 5.716A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.638A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.026A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.449A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.812A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.111A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.635A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 2970 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: 12.72 Time building geometry restraints manager: 8.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7804 1.34 - 1.47: 6732 1.47 - 1.59: 11428 1.59 - 1.72: 2 1.72 - 1.84: 136 Bond restraints: 26102 Sorted by residual: bond pdb=" CA ALA B 668 " pdb=" CB ALA B 668 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.54e-02 4.22e+03 1.66e+01 bond pdb=" CB ASN B 121 " pdb=" CG ASN B 121 " ideal model delta sigma weight residual 1.516 1.599 -0.083 2.50e-02 1.60e+03 1.11e+01 bond pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.93e+00 bond pdb=" N SER B 349 " pdb=" CA SER B 349 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.26e-02 6.30e+03 9.51e+00 bond pdb=" N GLU C 493 " pdb=" CA GLU C 493 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.13e+00 ... (remaining 26097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 34547 3.20 - 6.39: 863 6.39 - 9.59: 74 9.59 - 12.78: 13 12.78 - 15.98: 2 Bond angle restraints: 35499 Sorted by residual: angle pdb=" N ALA B 123 " pdb=" CA ALA B 123 " pdb=" C ALA B 123 " ideal model delta sigma weight residual 113.55 98.95 14.60 1.26e+00 6.30e-01 1.34e+02 angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 100.53 11.47 1.40e+00 5.10e-01 6.71e+01 angle pdb=" N TYR B 200 " pdb=" CA TYR B 200 " pdb=" C TYR B 200 " ideal model delta sigma weight residual 108.14 97.69 10.45 1.52e+00 4.33e-01 4.73e+01 angle pdb=" N ALA B 163 " pdb=" CA ALA B 163 " pdb=" C ALA B 163 " ideal model delta sigma weight residual 113.56 104.12 9.44 1.39e+00 5.18e-01 4.61e+01 angle pdb=" C ILE B 358 " pdb=" N SER B 359 " pdb=" CA SER B 359 " ideal model delta sigma weight residual 122.89 112.31 10.58 1.72e+00 3.38e-01 3.78e+01 ... (remaining 35494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 15285 21.32 - 42.64: 714 42.64 - 63.96: 184 63.96 - 85.27: 77 85.27 - 106.59: 37 Dihedral angle restraints: 16297 sinusoidal: 7126 harmonic: 9171 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 163.31 -70.31 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -146.62 60.62 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 52.25 40.75 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 16294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3344 0.075 - 0.151: 727 0.151 - 0.226: 84 0.226 - 0.302: 16 0.302 - 0.377: 5 Chirality restraints: 4176 Sorted by residual: chirality pdb=" CG LEU C 241 " pdb=" CB LEU C 241 " pdb=" CD1 LEU C 241 " pdb=" CD2 LEU C 241 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.10e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 30 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 4173 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 30 " -0.143 2.00e-02 2.50e+03 1.66e-01 3.46e+02 pdb=" CG ASN C 30 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 30 " 0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 30 " 0.271 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 30 " -0.089 2.00e-02 2.50e+03 9.54e-02 1.14e+02 pdb=" CG ASN B 30 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 30 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 30 " 0.147 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.112 2.00e-02 2.50e+03 9.50e-02 1.13e+02 pdb=" C7 NAG A1310 " -0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.153 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " 0.089 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 89 2.51 - 3.11: 18461 3.11 - 3.70: 37541 3.70 - 4.30: 56201 4.30 - 4.90: 93345 Nonbonded interactions: 205637 Sorted by model distance: nonbonded pdb=" OD1 ASP B 985 " pdb=" OE1 GLU B 988 " model vdw 1.909 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OD1 ASN C 394 " model vdw 1.951 3.040 nonbonded pdb=" O LEU A1141 " pdb=" CD1 LEU A1145 " model vdw 2.041 3.460 nonbonded pdb=" O GLY A 744 " pdb=" OD1 ASP A 745 " model vdw 2.067 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" CG ASN C 394 " model vdw 2.073 3.270 ... (remaining 205632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 65 or resid 74 through 138 or resid 157 through \ 173 or resid 188 through 350 or (resid 351 through 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 385 or res \ id 390 through 676 or resid 689 through 837 or resid 852 through 1150 or resid 1 \ 301 through 1306)) selection = (chain 'B' and (resid 26 through 676 or resid 689 through 837 or resid 852 throu \ gh 1150 or resid 1301 through 1306)) selection = (chain 'C' and (resid 26 through 65 or resid 74 through 138 or resid 157 through \ 173 or resid 188 through 350 or (resid 351 through 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 385 or res \ id 390 through 1150 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'L' selection = chain 'N' 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: 54.780 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: 0.050 Extract box with map and model: 1.540 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 69.700 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.480 26199 Z= 0.374 Angle : 1.229 36.259 35752 Z= 0.678 Chirality : 0.063 0.377 4176 Planarity : 0.008 0.170 4499 Dihedral : 14.913 106.592 10283 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.04 % Allowed : 11.38 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3104 helix: 1.42 (0.18), residues: 670 sheet: 1.03 (0.20), residues: 622 loop : -0.19 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 886 HIS 0.012 0.002 HIS A 339 PHE 0.042 0.003 PHE C 562 TYR 0.032 0.003 TYR A 269 ARG 0.016 0.002 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.01036 ( 38) link_NAG-ASN : angle 5.18465 ( 114) link_BETA1-4 : bond 0.00447 ( 21) link_BETA1-4 : angle 1.73188 ( 63) hydrogen bonds : bond 0.12903 ( 1028) hydrogen bonds : angle 7.56300 ( 2970) SS BOND : bond 0.09929 ( 38) SS BOND : angle 6.22843 ( 76) covalent geometry : bond 0.00692 (26102) covalent geometry : angle 1.16042 (35499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8384 (p) cc_final: 0.7900 (m) REVERT: A 493 GLU cc_start: 0.5114 (pp20) cc_final: 0.4895 (pp20) REVERT: A 529 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8452 (mtpt) REVERT: A 1010 GLN cc_start: 0.8145 (mp10) cc_final: 0.7156 (mp10) REVERT: A 1119 ASN cc_start: 0.7353 (m-40) cc_final: 0.7145 (m110) REVERT: B 41 LYS cc_start: 0.7680 (mmtp) cc_final: 0.7403 (mmpt) REVERT: B 239 GLN cc_start: 0.8444 (tt0) cc_final: 0.8105 (tt0) REVERT: B 432 CYS cc_start: 0.6047 (m) cc_final: 0.5583 (m) REVERT: B 646 ARG cc_start: 0.7882 (tpp-160) cc_final: 0.7417 (tpp80) REVERT: B 900 MET cc_start: 0.8710 (mtp) cc_final: 0.7905 (mtm) REVERT: B 1038 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8544 (mptt) REVERT: B 1092 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 1142 GLN cc_start: 0.6955 (mm110) cc_final: 0.6485 (tp40) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 1.1441 time to fit residues: 424.1811 Evaluate side-chains 262 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 641 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 246 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 564 GLN A1101 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 505 HIS C 26 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 641 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125599 restraints weight = 30619.292| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.76 r_work: 0.3236 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 26199 Z= 0.153 Angle : 0.702 12.193 35752 Z= 0.351 Chirality : 0.050 0.688 4176 Planarity : 0.004 0.066 4499 Dihedral : 8.417 64.786 4597 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.28 % Allowed : 10.08 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3104 helix: 2.49 (0.19), residues: 673 sheet: 0.65 (0.19), residues: 651 loop : -0.38 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 452 HIS 0.006 0.001 HIS A 68 PHE 0.018 0.002 PHE A 186 TYR 0.022 0.001 TYR B 904 ARG 0.007 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.01456 ( 38) link_NAG-ASN : angle 3.53654 ( 114) link_BETA1-4 : bond 0.00745 ( 21) link_BETA1-4 : angle 2.24919 ( 63) hydrogen bonds : bond 0.04783 ( 1028) hydrogen bonds : angle 5.93262 ( 2970) SS BOND : bond 0.00461 ( 38) SS BOND : angle 1.54120 ( 76) covalent geometry : bond 0.00340 (26102) covalent geometry : angle 0.66529 (35499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8526 (p) cc_final: 0.8227 (m) REVERT: A 200 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6874 (m-80) REVERT: A 237 ARG cc_start: 0.7274 (mtp-110) cc_final: 0.6715 (mtt90) REVERT: A 241 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5376 (mp) REVERT: A 298 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 493 GLU cc_start: 0.5085 (pp20) cc_final: 0.4676 (pp20) REVERT: A 516 GLU cc_start: 0.7159 (tt0) cc_final: 0.6934 (tt0) REVERT: A 529 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8524 (mtpt) REVERT: A 574 ASP cc_start: 0.8589 (t0) cc_final: 0.8358 (t0) REVERT: A 618 THR cc_start: 0.8281 (m) cc_final: 0.8042 (p) REVERT: A 794 ILE cc_start: 0.8666 (mp) cc_final: 0.8351 (mm) REVERT: A 994 ASP cc_start: 0.7633 (m-30) cc_final: 0.7279 (t70) REVERT: A 1119 ASN cc_start: 0.7682 (m-40) cc_final: 0.7457 (m110) REVERT: B 41 LYS cc_start: 0.7436 (mmtp) cc_final: 0.7016 (mmpt) REVERT: B 128 ILE cc_start: 0.7704 (mt) cc_final: 0.7448 (mp) REVERT: B 202 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7170 (mptt) REVERT: B 233 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7071 (tp) REVERT: B 355 ARG cc_start: 0.6324 (mmt-90) cc_final: 0.5861 (mmt-90) REVERT: B 646 ARG cc_start: 0.8170 (tpp-160) cc_final: 0.7641 (mpp80) REVERT: B 1010 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 1017 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: B 1038 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8737 (mptt) REVERT: B 1092 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 1101 HIS cc_start: 0.8836 (m90) cc_final: 0.8594 (m90) REVERT: B 1119 ASN cc_start: 0.7981 (m-40) cc_final: 0.7651 (m-40) REVERT: B 1142 GLN cc_start: 0.6744 (mm110) cc_final: 0.6057 (tp40) REVERT: C 658 ASN cc_start: 0.8378 (m-40) cc_final: 0.8022 (m-40) REVERT: C 1010 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8156 (mp10) outliers start: 63 outliers final: 23 residues processed: 338 average time/residue: 0.9718 time to fit residues: 400.7631 Evaluate side-chains 288 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 257 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 298 optimal weight: 0.4980 chunk 260 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1071 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118075 restraints weight = 30670.976| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.44 r_work: 0.3140 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 26199 Z= 0.208 Angle : 0.686 15.974 35752 Z= 0.343 Chirality : 0.050 0.453 4176 Planarity : 0.004 0.050 4499 Dihedral : 6.270 49.564 4595 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.83 % Allowed : 10.66 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3104 helix: 2.27 (0.19), residues: 689 sheet: 0.46 (0.19), residues: 693 loop : -0.64 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 452 HIS 0.006 0.001 HIS A1058 PHE 0.022 0.002 PHE C 562 TYR 0.025 0.002 TYR B1067 ARG 0.008 0.001 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 38) link_NAG-ASN : angle 3.69333 ( 114) link_BETA1-4 : bond 0.00669 ( 21) link_BETA1-4 : angle 2.05732 ( 63) hydrogen bonds : bond 0.04962 ( 1028) hydrogen bonds : angle 5.76405 ( 2970) SS BOND : bond 0.00604 ( 38) SS BOND : angle 1.60115 ( 76) covalent geometry : bond 0.00498 (26102) covalent geometry : angle 0.64636 (35499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 283 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8650 (p) cc_final: 0.8328 (m) REVERT: A 200 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: A 237 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.6893 (mtt90) REVERT: A 271 GLN cc_start: 0.8547 (mt0) cc_final: 0.8255 (mt0) REVERT: A 465 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7956 (tt0) REVERT: A 493 GLU cc_start: 0.5028 (pp20) cc_final: 0.4539 (pp20) REVERT: A 529 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8523 (mtpt) REVERT: A 574 ASP cc_start: 0.8580 (t0) cc_final: 0.8331 (t0) REVERT: A 618 THR cc_start: 0.8511 (m) cc_final: 0.8265 (p) REVERT: A 765 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7554 (ttm110) REVERT: A 779 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: A 794 ILE cc_start: 0.8712 (mp) cc_final: 0.8393 (mm) REVERT: A 994 ASP cc_start: 0.7675 (m-30) cc_final: 0.7407 (t70) REVERT: A 1010 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: A 1092 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8681 (mt-10) REVERT: A 1142 GLN cc_start: 0.7216 (mm110) cc_final: 0.6923 (mm110) REVERT: B 41 LYS cc_start: 0.7469 (mmtp) cc_final: 0.7047 (mmpt) REVERT: B 128 ILE cc_start: 0.7647 (mt) cc_final: 0.7375 (mp) REVERT: B 168 PHE cc_start: 0.7485 (t80) cc_final: 0.7223 (t80) REVERT: B 169 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7462 (tp30) REVERT: B 202 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7251 (mptt) REVERT: B 233 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7117 (tp) REVERT: B 355 ARG cc_start: 0.6578 (mmt-90) cc_final: 0.6043 (mmt-90) REVERT: B 574 ASP cc_start: 0.8277 (p0) cc_final: 0.8008 (p0) REVERT: B 646 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.7569 (mtm180) REVERT: B 735 SER cc_start: 0.8773 (t) cc_final: 0.8404 (p) REVERT: B 904 TYR cc_start: 0.8275 (m-80) cc_final: 0.7209 (m-80) REVERT: B 1010 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: B 1017 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: B 1038 LYS cc_start: 0.8993 (mmtp) cc_final: 0.8636 (mptt) REVERT: B 1092 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8234 (mt-10) REVERT: B 1142 GLN cc_start: 0.6767 (mm110) cc_final: 0.6124 (tp40) REVERT: C 94 SER cc_start: 0.8064 (p) cc_final: 0.7711 (m) REVERT: C 237 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7718 (mtm110) REVERT: C 408 SER cc_start: 0.5775 (OUTLIER) cc_final: 0.5408 (p) REVERT: C 1010 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: C 1086 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8276 (mtpp) outliers start: 78 outliers final: 30 residues processed: 337 average time/residue: 1.0366 time to fit residues: 422.5150 Evaluate side-chains 288 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 241 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 675 GLN B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119285 restraints weight = 30905.491| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.43 r_work: 0.3179 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26199 Z= 0.148 Angle : 0.603 12.840 35752 Z= 0.302 Chirality : 0.047 0.473 4176 Planarity : 0.004 0.053 4499 Dihedral : 5.312 56.896 4595 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.68 % Allowed : 12.18 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3104 helix: 2.38 (0.19), residues: 688 sheet: 0.37 (0.19), residues: 671 loop : -0.66 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 452 HIS 0.004 0.001 HIS A1058 PHE 0.020 0.001 PHE C 562 TYR 0.023 0.001 TYR B 170 ARG 0.005 0.000 ARG C 34 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 38) link_NAG-ASN : angle 3.26057 ( 114) link_BETA1-4 : bond 0.00596 ( 21) link_BETA1-4 : angle 1.73142 ( 63) hydrogen bonds : bond 0.04281 ( 1028) hydrogen bonds : angle 5.54847 ( 2970) SS BOND : bond 0.00297 ( 38) SS BOND : angle 1.42989 ( 76) covalent geometry : bond 0.00346 (26102) covalent geometry : angle 0.56761 (35499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 260 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8667 (p) cc_final: 0.8403 (m) REVERT: A 200 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 237 ARG cc_start: 0.7392 (mtp-110) cc_final: 0.6909 (mtt90) REVERT: A 269 TYR cc_start: 0.8491 (m-80) cc_final: 0.8282 (m-80) REVERT: A 271 GLN cc_start: 0.8539 (mt0) cc_final: 0.8244 (mt0) REVERT: A 465 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8018 (tt0) REVERT: A 493 GLU cc_start: 0.5080 (pp20) cc_final: 0.4524 (pp20) REVERT: A 529 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8506 (mtpt) REVERT: A 574 ASP cc_start: 0.8480 (t0) cc_final: 0.8236 (t0) REVERT: A 765 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7416 (mtm-85) REVERT: A 779 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8261 (tp40) REVERT: A 794 ILE cc_start: 0.8686 (mp) cc_final: 0.8400 (mm) REVERT: A 994 ASP cc_start: 0.7634 (m-30) cc_final: 0.7384 (t70) REVERT: A 1010 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: A 1092 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8660 (mt-10) REVERT: A 1142 GLN cc_start: 0.7235 (mm110) cc_final: 0.6906 (mm-40) REVERT: B 41 LYS cc_start: 0.7397 (mmtp) cc_final: 0.6981 (mmpt) REVERT: B 128 ILE cc_start: 0.7698 (mt) cc_final: 0.7480 (mp) REVERT: B 202 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7137 (mptt) REVERT: B 233 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7113 (tp) REVERT: B 335 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7063 (tp) REVERT: B 574 ASP cc_start: 0.8268 (p0) cc_final: 0.7973 (p0) REVERT: B 646 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7650 (mtm180) REVERT: B 735 SER cc_start: 0.8742 (t) cc_final: 0.8369 (p) REVERT: B 1010 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: B 1038 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8644 (mptt) REVERT: B 1092 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 1142 GLN cc_start: 0.6740 (mm110) cc_final: 0.6082 (tp40) REVERT: C 94 SER cc_start: 0.7974 (p) cc_final: 0.7721 (m) REVERT: C 102 ARG cc_start: 0.6673 (ptm160) cc_final: 0.5796 (mmt-90) REVERT: C 205 SER cc_start: 0.9341 (p) cc_final: 0.8995 (t) REVERT: C 226 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (tt) REVERT: C 377 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.5443 (m-80) REVERT: C 408 SER cc_start: 0.5828 (OUTLIER) cc_final: 0.5526 (p) REVERT: C 554 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7299 (mtpt) REVERT: C 581 THR cc_start: 0.8291 (p) cc_final: 0.8079 (t) REVERT: C 646 ARG cc_start: 0.8306 (mmt180) cc_final: 0.8013 (tpp80) REVERT: C 854 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5744 (mtmt) REVERT: C 990 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: C 1010 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: C 1086 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8095 (mtpp) REVERT: C 1119 ASN cc_start: 0.7992 (m-40) cc_final: 0.7751 (m-40) outliers start: 74 outliers final: 32 residues processed: 311 average time/residue: 0.9953 time to fit residues: 377.6474 Evaluate side-chains 286 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 267 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 chunk 259 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN A 439 ASN A 506 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115983 restraints weight = 30889.801| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.38 r_work: 0.3132 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 26199 Z= 0.208 Angle : 0.640 11.524 35752 Z= 0.322 Chirality : 0.049 0.512 4176 Planarity : 0.004 0.051 4499 Dihedral : 5.277 50.947 4595 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 3.01 % Allowed : 12.47 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3104 helix: 2.18 (0.19), residues: 698 sheet: 0.33 (0.19), residues: 681 loop : -0.83 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 452 HIS 0.006 0.001 HIS A1058 PHE 0.019 0.002 PHE C 898 TYR 0.024 0.001 TYR B1067 ARG 0.005 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 38) link_NAG-ASN : angle 3.30403 ( 114) link_BETA1-4 : bond 0.00499 ( 21) link_BETA1-4 : angle 1.61114 ( 63) hydrogen bonds : bond 0.04760 ( 1028) hydrogen bonds : angle 5.61634 ( 2970) SS BOND : bond 0.00439 ( 38) SS BOND : angle 1.52352 ( 76) covalent geometry : bond 0.00504 (26102) covalent geometry : angle 0.60687 (35499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 250 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8770 (p) cc_final: 0.8362 (m) REVERT: A 237 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6982 (mtt90) REVERT: A 269 TYR cc_start: 0.8467 (m-80) cc_final: 0.8144 (m-80) REVERT: A 271 GLN cc_start: 0.8543 (mt0) cc_final: 0.8234 (mt0) REVERT: A 465 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8048 (tt0) REVERT: A 493 GLU cc_start: 0.5107 (pp20) cc_final: 0.4558 (pp20) REVERT: A 529 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8424 (mtpt) REVERT: A 574 ASP cc_start: 0.8501 (t0) cc_final: 0.8231 (t0) REVERT: A 765 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7487 (ttm110) REVERT: A 779 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8258 (tp40) REVERT: A 794 ILE cc_start: 0.8676 (mp) cc_final: 0.8393 (mm) REVERT: A 994 ASP cc_start: 0.7711 (m-30) cc_final: 0.7467 (t70) REVERT: A 1010 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: A 1092 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8712 (mt-10) REVERT: A 1142 GLN cc_start: 0.7325 (mm110) cc_final: 0.6971 (mm110) REVERT: B 41 LYS cc_start: 0.7542 (mmtp) cc_final: 0.6957 (mmpt) REVERT: B 128 ILE cc_start: 0.7717 (mt) cc_final: 0.7487 (mp) REVERT: B 202 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7239 (mptt) REVERT: B 233 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7113 (tp) REVERT: B 574 ASP cc_start: 0.8383 (p0) cc_final: 0.8086 (p0) REVERT: B 646 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7723 (mtm180) REVERT: B 735 SER cc_start: 0.8762 (t) cc_final: 0.8406 (p) REVERT: B 904 TYR cc_start: 0.8194 (m-80) cc_final: 0.7073 (m-80) REVERT: B 929 SER cc_start: 0.8507 (t) cc_final: 0.8207 (p) REVERT: B 1010 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: B 1038 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8642 (mptt) REVERT: B 1092 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 1142 GLN cc_start: 0.6729 (mm110) cc_final: 0.6072 (tp40) REVERT: C 102 ARG cc_start: 0.6716 (ptm160) cc_final: 0.5807 (mmt-90) REVERT: C 197 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 205 SER cc_start: 0.9344 (p) cc_final: 0.9020 (t) REVERT: C 226 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (tt) REVERT: C 377 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: C 408 SER cc_start: 0.5852 (OUTLIER) cc_final: 0.5559 (p) REVERT: C 646 ARG cc_start: 0.8334 (mmt180) cc_final: 0.8026 (mpp-170) REVERT: C 854 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5834 (mtmt) REVERT: C 934 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 950 ASP cc_start: 0.8236 (m-30) cc_final: 0.7943 (m-30) REVERT: C 1010 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: C 1086 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8096 (mtpp) outliers start: 83 outliers final: 48 residues processed: 314 average time/residue: 1.0043 time to fit residues: 385.7920 Evaluate side-chains 291 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1142 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 269 optimal weight: 5.9990 chunk 240 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117698 restraints weight = 30731.249| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.40 r_work: 0.3159 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26199 Z= 0.145 Angle : 0.592 14.968 35752 Z= 0.296 Chirality : 0.047 0.542 4176 Planarity : 0.004 0.054 4499 Dihedral : 5.059 53.039 4595 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 2.90 % Allowed : 13.01 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3104 helix: 2.34 (0.19), residues: 696 sheet: 0.31 (0.19), residues: 681 loop : -0.82 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 452 HIS 0.003 0.001 HIS A1058 PHE 0.016 0.001 PHE B 562 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 38) link_NAG-ASN : angle 3.26279 ( 114) link_BETA1-4 : bond 0.00552 ( 21) link_BETA1-4 : angle 1.47746 ( 63) hydrogen bonds : bond 0.04238 ( 1028) hydrogen bonds : angle 5.47542 ( 2970) SS BOND : bond 0.00301 ( 38) SS BOND : angle 1.38171 ( 76) covalent geometry : bond 0.00341 (26102) covalent geometry : angle 0.55732 (35499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 243 time to evaluate : 2.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8755 (p) cc_final: 0.8371 (m) REVERT: A 237 ARG cc_start: 0.7377 (mtp-110) cc_final: 0.6945 (mtt90) REVERT: A 269 TYR cc_start: 0.8434 (m-80) cc_final: 0.8112 (m-80) REVERT: A 271 GLN cc_start: 0.8504 (mt0) cc_final: 0.8203 (mt0) REVERT: A 465 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8042 (tt0) REVERT: A 493 GLU cc_start: 0.5147 (pp20) cc_final: 0.4653 (pp20) REVERT: A 529 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: A 564 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7301 (mm-40) REVERT: A 574 ASP cc_start: 0.8471 (t0) cc_final: 0.8140 (t0) REVERT: A 765 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7445 (ttm110) REVERT: A 779 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: A 794 ILE cc_start: 0.8667 (mp) cc_final: 0.8404 (mm) REVERT: A 994 ASP cc_start: 0.7670 (m-30) cc_final: 0.7422 (t70) REVERT: A 1010 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: A 1092 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8681 (mt-10) REVERT: A 1142 GLN cc_start: 0.7354 (mm110) cc_final: 0.7022 (mm110) REVERT: B 41 LYS cc_start: 0.7498 (mmtp) cc_final: 0.6926 (mmpt) REVERT: B 202 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7172 (mptt) REVERT: B 233 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7106 (tp) REVERT: B 574 ASP cc_start: 0.8319 (p0) cc_final: 0.8058 (p0) REVERT: B 646 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7735 (mtm180) REVERT: B 735 SER cc_start: 0.8751 (t) cc_final: 0.8390 (p) REVERT: B 904 TYR cc_start: 0.8133 (m-80) cc_final: 0.7078 (m-80) REVERT: B 1010 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: B 1038 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8629 (mptt) REVERT: B 1092 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 1142 GLN cc_start: 0.6728 (mm110) cc_final: 0.6068 (tp40) REVERT: C 102 ARG cc_start: 0.6692 (ptm160) cc_final: 0.5808 (mmt-90) REVERT: C 205 SER cc_start: 0.9333 (p) cc_final: 0.9038 (t) REVERT: C 226 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (tt) REVERT: C 377 PHE cc_start: 0.5997 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: C 408 SER cc_start: 0.5877 (OUTLIER) cc_final: 0.5633 (p) REVERT: C 554 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7291 (mtpt) REVERT: C 646 ARG cc_start: 0.8306 (mmt180) cc_final: 0.8018 (mpp-170) REVERT: C 854 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5915 (mtmt) REVERT: C 934 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 1010 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: C 1143 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6871 (mp) outliers start: 80 outliers final: 38 residues processed: 303 average time/residue: 0.9722 time to fit residues: 362.0371 Evaluate side-chains 280 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 554 LYS Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 160 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 304 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 GLN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117114 restraints weight = 30984.661| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.40 r_work: 0.3141 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26199 Z= 0.188 Angle : 0.631 14.472 35752 Z= 0.314 Chirality : 0.048 0.594 4176 Planarity : 0.004 0.054 4499 Dihedral : 5.112 53.989 4595 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 3.19 % Allowed : 13.27 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3104 helix: 2.25 (0.19), residues: 701 sheet: 0.27 (0.19), residues: 683 loop : -0.89 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 452 HIS 0.005 0.001 HIS A1058 PHE 0.017 0.001 PHE B 898 TYR 0.022 0.001 TYR B1067 ARG 0.005 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 38) link_NAG-ASN : angle 3.75681 ( 114) link_BETA1-4 : bond 0.00543 ( 21) link_BETA1-4 : angle 1.48151 ( 63) hydrogen bonds : bond 0.04479 ( 1028) hydrogen bonds : angle 5.50498 ( 2970) SS BOND : bond 0.00379 ( 38) SS BOND : angle 1.43221 ( 76) covalent geometry : bond 0.00453 (26102) covalent geometry : angle 0.58983 (35499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8784 (p) cc_final: 0.8336 (m) REVERT: A 237 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.6999 (mtt90) REVERT: A 269 TYR cc_start: 0.8447 (m-80) cc_final: 0.8088 (m-80) REVERT: A 271 GLN cc_start: 0.8496 (mt0) cc_final: 0.8235 (mt0) REVERT: A 357 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7753 (ttt90) REVERT: A 465 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8082 (tt0) REVERT: A 493 GLU cc_start: 0.5178 (pp20) cc_final: 0.4660 (pp20) REVERT: A 529 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8461 (mtpt) REVERT: A 564 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7326 (mm-40) REVERT: A 574 ASP cc_start: 0.8495 (t0) cc_final: 0.8145 (t0) REVERT: A 765 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7481 (ttm110) REVERT: A 779 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8260 (tp40) REVERT: A 794 ILE cc_start: 0.8666 (mp) cc_final: 0.8400 (mm) REVERT: A 994 ASP cc_start: 0.7683 (m-30) cc_final: 0.7417 (t70) REVERT: A 1010 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: A 1092 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8716 (mt-10) REVERT: A 1142 GLN cc_start: 0.7413 (mm110) cc_final: 0.7113 (mm110) REVERT: B 41 LYS cc_start: 0.7539 (mmtp) cc_final: 0.6913 (mmpt) REVERT: B 129 LYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6706 (ttpt) REVERT: B 169 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: B 202 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7335 (mptt) REVERT: B 233 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7089 (tp) REVERT: B 574 ASP cc_start: 0.8310 (p0) cc_final: 0.8052 (p0) REVERT: B 646 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.7763 (mtm180) REVERT: B 735 SER cc_start: 0.8768 (t) cc_final: 0.8326 (p) REVERT: B 904 TYR cc_start: 0.8119 (m-80) cc_final: 0.7056 (m-80) REVERT: B 929 SER cc_start: 0.8496 (t) cc_final: 0.8200 (p) REVERT: B 1010 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: B 1038 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8631 (mptt) REVERT: B 1092 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 102 ARG cc_start: 0.6684 (ptm160) cc_final: 0.5793 (mmt-90) REVERT: C 205 SER cc_start: 0.9339 (p) cc_final: 0.9040 (t) REVERT: C 226 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 377 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: C 408 SER cc_start: 0.5845 (OUTLIER) cc_final: 0.5635 (p) REVERT: C 454 ARG cc_start: 0.5394 (ttm170) cc_final: 0.4931 (ttm170) REVERT: C 501 TYR cc_start: 0.4851 (OUTLIER) cc_final: 0.2925 (m-80) REVERT: C 646 ARG cc_start: 0.8335 (mmt180) cc_final: 0.8028 (mpp-170) REVERT: C 934 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7714 (mp) REVERT: C 1010 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: C 1143 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6719 (mp) outliers start: 88 outliers final: 46 residues processed: 306 average time/residue: 1.0115 time to fit residues: 375.1924 Evaluate side-chains 292 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 230 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 22 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 143 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 85 optimal weight: 0.0030 chunk 132 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 26 GLN C 271 GLN C 280 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119152 restraints weight = 30635.596| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.44 r_work: 0.3185 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26199 Z= 0.112 Angle : 0.578 12.118 35752 Z= 0.289 Chirality : 0.046 0.515 4176 Planarity : 0.004 0.056 4499 Dihedral : 4.857 56.672 4595 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.46 % Allowed : 14.10 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3104 helix: 2.45 (0.19), residues: 706 sheet: 0.31 (0.19), residues: 679 loop : -0.79 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 452 HIS 0.003 0.000 HIS A 519 PHE 0.016 0.001 PHE B 759 TYR 0.022 0.001 TYR A 170 ARG 0.009 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 38) link_NAG-ASN : angle 3.46704 ( 114) link_BETA1-4 : bond 0.00530 ( 21) link_BETA1-4 : angle 1.37337 ( 63) hydrogen bonds : bond 0.03890 ( 1028) hydrogen bonds : angle 5.31943 ( 2970) SS BOND : bond 0.00217 ( 38) SS BOND : angle 1.29977 ( 76) covalent geometry : bond 0.00247 (26102) covalent geometry : angle 0.53890 (35499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 253 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8736 (p) cc_final: 0.8363 (m) REVERT: A 237 ARG cc_start: 0.7273 (mtp-110) cc_final: 0.6896 (mtt90) REVERT: A 269 TYR cc_start: 0.8385 (m-80) cc_final: 0.8019 (m-80) REVERT: A 271 GLN cc_start: 0.8444 (mt0) cc_final: 0.7837 (mm-40) REVERT: A 357 ARG cc_start: 0.8110 (ttt-90) cc_final: 0.7717 (ttt90) REVERT: A 465 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8058 (tt0) REVERT: A 493 GLU cc_start: 0.5121 (pp20) cc_final: 0.4616 (pp20) REVERT: A 529 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8446 (mtpt) REVERT: A 574 ASP cc_start: 0.8410 (t0) cc_final: 0.8133 (t0) REVERT: A 765 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7380 (mtm-85) REVERT: A 779 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8194 (tp40) REVERT: A 794 ILE cc_start: 0.8638 (mp) cc_final: 0.8366 (mm) REVERT: A 994 ASP cc_start: 0.7548 (m-30) cc_final: 0.7283 (t70) REVERT: A 1010 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: A 1092 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8690 (mt-10) REVERT: A 1142 GLN cc_start: 0.7417 (mm110) cc_final: 0.7201 (mm110) REVERT: B 41 LYS cc_start: 0.7460 (mmtp) cc_final: 0.6906 (mmpt) REVERT: B 202 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7085 (mptt) REVERT: B 233 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7068 (tp) REVERT: B 355 ARG cc_start: 0.6476 (mmt-90) cc_final: 0.6249 (mmt-90) REVERT: B 646 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.7729 (mtm180) REVERT: B 735 SER cc_start: 0.8746 (t) cc_final: 0.8274 (p) REVERT: B 904 TYR cc_start: 0.8010 (m-80) cc_final: 0.7003 (m-80) REVERT: B 1010 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.6858 (mp10) REVERT: B 1092 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 102 ARG cc_start: 0.6559 (ptm160) cc_final: 0.5747 (mmt-90) REVERT: C 205 SER cc_start: 0.9316 (p) cc_final: 0.9048 (t) REVERT: C 226 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (tt) REVERT: C 377 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5645 (m-80) REVERT: C 501 TYR cc_start: 0.4827 (OUTLIER) cc_final: 0.2912 (m-80) REVERT: C 646 ARG cc_start: 0.8295 (mmt180) cc_final: 0.8007 (mpp-170) REVERT: C 947 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8549 (mmmt) REVERT: C 1010 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: C 1119 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7605 (p0) outliers start: 68 outliers final: 30 residues processed: 298 average time/residue: 1.0407 time to fit residues: 378.3860 Evaluate side-chains 276 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 296 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 138 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS B 280 ASN C 26 GLN C 271 GLN C 280 ASN C 409 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.168426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118316 restraints weight = 30843.779| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.61 r_work: 0.3152 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26199 Z= 0.163 Angle : 0.616 19.488 35752 Z= 0.305 Chirality : 0.049 0.729 4176 Planarity : 0.004 0.057 4499 Dihedral : 4.933 57.425 4595 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 2.10 % Allowed : 14.93 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3104 helix: 2.37 (0.19), residues: 704 sheet: 0.29 (0.19), residues: 679 loop : -0.86 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 452 HIS 0.004 0.001 HIS C1058 PHE 0.017 0.001 PHE B 898 TYR 0.022 0.001 TYR B1067 ARG 0.007 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 38) link_NAG-ASN : angle 3.79894 ( 114) link_BETA1-4 : bond 0.00522 ( 21) link_BETA1-4 : angle 1.38667 ( 63) hydrogen bonds : bond 0.04254 ( 1028) hydrogen bonds : angle 5.38599 ( 2970) SS BOND : bond 0.00350 ( 38) SS BOND : angle 1.37722 ( 76) covalent geometry : bond 0.00396 (26102) covalent geometry : angle 0.57265 (35499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8765 (p) cc_final: 0.8340 (m) REVERT: A 237 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.6926 (mtt90) REVERT: A 269 TYR cc_start: 0.8388 (m-80) cc_final: 0.8001 (m-80) REVERT: A 271 GLN cc_start: 0.8454 (mt0) cc_final: 0.8202 (mt0) REVERT: A 357 ARG cc_start: 0.8105 (ttt-90) cc_final: 0.7700 (ttt90) REVERT: A 465 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8113 (tt0) REVERT: A 493 GLU cc_start: 0.5187 (pp20) cc_final: 0.4662 (pp20) REVERT: A 529 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (mtpt) REVERT: A 574 ASP cc_start: 0.8451 (t0) cc_final: 0.8105 (t0) REVERT: A 765 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7597 (ttp-110) REVERT: A 779 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8215 (tp40) REVERT: A 794 ILE cc_start: 0.8655 (mp) cc_final: 0.8397 (mm) REVERT: A 855 PHE cc_start: 0.4817 (m-80) cc_final: 0.4597 (m-80) REVERT: A 994 ASP cc_start: 0.7623 (m-30) cc_final: 0.7353 (t70) REVERT: A 1010 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7631 (mp10) REVERT: A 1092 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8695 (mt-10) REVERT: A 1142 GLN cc_start: 0.7425 (mm110) cc_final: 0.7098 (mm-40) REVERT: B 41 LYS cc_start: 0.7497 (mmtp) cc_final: 0.6903 (mmpt) REVERT: B 202 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7283 (mptt) REVERT: B 233 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 574 ASP cc_start: 0.8176 (p0) cc_final: 0.7950 (p0) REVERT: B 646 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7738 (mtm180) REVERT: B 735 SER cc_start: 0.8756 (t) cc_final: 0.8302 (p) REVERT: B 904 TYR cc_start: 0.8090 (m-80) cc_final: 0.7049 (m-80) REVERT: B 929 SER cc_start: 0.8479 (t) cc_final: 0.8197 (p) REVERT: B 1010 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: B 1092 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 1142 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6288 (tp-100) REVERT: C 26 GLN cc_start: 0.5710 (OUTLIER) cc_final: 0.4879 (pm20) REVERT: C 102 ARG cc_start: 0.6609 (ptm160) cc_final: 0.5768 (mmt-90) REVERT: C 205 SER cc_start: 0.9314 (p) cc_final: 0.9050 (t) REVERT: C 226 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 377 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5651 (m-80) REVERT: C 501 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.3071 (m-80) REVERT: C 646 ARG cc_start: 0.8317 (mmt180) cc_final: 0.8009 (mpp-170) REVERT: C 947 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8675 (mmmt) REVERT: C 1010 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8135 (mp10) outliers start: 58 outliers final: 40 residues processed: 280 average time/residue: 1.0882 time to fit residues: 370.9506 Evaluate side-chains 282 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 193 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 288 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN B 280 ASN C 26 GLN C 271 GLN C 280 ASN C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.169151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117930 restraints weight = 30755.192| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.39 r_work: 0.3170 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26199 Z= 0.136 Angle : 0.610 17.534 35752 Z= 0.302 Chirality : 0.049 0.959 4176 Planarity : 0.004 0.057 4499 Dihedral : 4.914 57.780 4595 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 14.90 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3104 helix: 2.41 (0.19), residues: 704 sheet: 0.28 (0.19), residues: 679 loop : -0.84 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 452 HIS 0.003 0.001 HIS A 519 PHE 0.041 0.001 PHE C 562 TYR 0.021 0.001 TYR B1067 ARG 0.008 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 38) link_NAG-ASN : angle 3.95168 ( 114) link_BETA1-4 : bond 0.00532 ( 21) link_BETA1-4 : angle 1.35310 ( 63) hydrogen bonds : bond 0.04079 ( 1028) hydrogen bonds : angle 5.35160 ( 2970) SS BOND : bond 0.00301 ( 38) SS BOND : angle 1.34050 ( 76) covalent geometry : bond 0.00321 (26102) covalent geometry : angle 0.56303 (35499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 235 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8759 (p) cc_final: 0.8349 (m) REVERT: A 237 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.6954 (mtt90) REVERT: A 269 TYR cc_start: 0.8399 (m-80) cc_final: 0.8028 (m-80) REVERT: A 271 GLN cc_start: 0.8449 (mt0) cc_final: 0.8204 (mt0) REVERT: A 357 ARG cc_start: 0.8114 (ttt-90) cc_final: 0.7719 (ttt90) REVERT: A 465 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8114 (tt0) REVERT: A 493 GLU cc_start: 0.5234 (pp20) cc_final: 0.4712 (pp20) REVERT: A 529 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8445 (mtpt) REVERT: A 574 ASP cc_start: 0.8443 (t0) cc_final: 0.8135 (t0) REVERT: A 765 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7422 (mtm-85) REVERT: A 779 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8224 (tp40) REVERT: A 794 ILE cc_start: 0.8658 (mp) cc_final: 0.8403 (mm) REVERT: A 855 PHE cc_start: 0.4855 (m-80) cc_final: 0.4602 (m-80) REVERT: A 994 ASP cc_start: 0.7624 (m-30) cc_final: 0.7352 (t70) REVERT: A 1010 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: A 1092 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 41 LYS cc_start: 0.7507 (mmtp) cc_final: 0.6963 (mmpt) REVERT: B 74 ASN cc_start: 0.4893 (OUTLIER) cc_final: 0.4466 (m110) REVERT: B 202 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7323 (mptt) REVERT: B 233 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 310 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8790 (tttm) REVERT: B 574 ASP cc_start: 0.8190 (p0) cc_final: 0.7960 (p0) REVERT: B 646 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.7779 (mtm180) REVERT: B 735 SER cc_start: 0.8749 (t) cc_final: 0.8318 (p) REVERT: B 904 TYR cc_start: 0.8049 (m-80) cc_final: 0.7042 (m-80) REVERT: B 929 SER cc_start: 0.8504 (t) cc_final: 0.8237 (p) REVERT: B 1010 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: B 1092 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 1142 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6206 (tp-100) REVERT: C 26 GLN cc_start: 0.6032 (OUTLIER) cc_final: 0.5688 (pm20) REVERT: C 102 ARG cc_start: 0.6631 (ptm160) cc_final: 0.5775 (mmt-90) REVERT: C 205 SER cc_start: 0.9319 (p) cc_final: 0.9069 (t) REVERT: C 226 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8157 (tt) REVERT: C 377 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: C 501 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.3184 (m-80) REVERT: C 646 ARG cc_start: 0.8320 (mmt180) cc_final: 0.8058 (mpp-170) REVERT: C 947 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8685 (mmmt) REVERT: C 1010 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8154 (mp10) outliers start: 61 outliers final: 39 residues processed: 277 average time/residue: 1.2066 time to fit residues: 406.3744 Evaluate side-chains 281 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 GLN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 178 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 307 optimal weight: 0.0870 chunk 164 optimal weight: 4.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 913 GLN B 280 ASN B1071 GLN C 26 GLN C 271 GLN C 280 ASN C 556 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120959 restraints weight = 30684.089| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.69 r_work: 0.3183 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 26199 Z= 0.111 Angle : 0.583 14.198 35752 Z= 0.290 Chirality : 0.047 0.750 4176 Planarity : 0.004 0.058 4499 Dihedral : 4.799 56.864 4595 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.92 % Allowed : 15.19 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3104 helix: 2.57 (0.19), residues: 699 sheet: 0.27 (0.19), residues: 676 loop : -0.78 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 452 HIS 0.002 0.000 HIS A 519 PHE 0.034 0.001 PHE C 562 TYR 0.020 0.001 TYR B1067 ARG 0.008 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 38) link_NAG-ASN : angle 3.50892 ( 114) link_BETA1-4 : bond 0.00519 ( 21) link_BETA1-4 : angle 1.29829 ( 63) hydrogen bonds : bond 0.03770 ( 1028) hydrogen bonds : angle 5.23379 ( 2970) SS BOND : bond 0.00237 ( 38) SS BOND : angle 1.28583 ( 76) covalent geometry : bond 0.00248 (26102) covalent geometry : angle 0.54456 (35499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18806.94 seconds wall clock time: 324 minutes 8.52 seconds (19448.52 seconds total)