Starting phenix.real_space_refine on Fri Jun 20 00:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.map" model { file = "/net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jzl_22532/06_2025/7jzl_22532.cif" } resolution = 2.7 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= 0.004 sd= 0.079 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 102 5.16 5 C 14661 2.51 5 N 3858 2.21 5 O 4502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 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: 23123 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 980, 7420 Classifications: {'peptide': 980} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 53, 'TRANS': 926} Chain breaks: 10 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Chain: "E" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 6978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 6978 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PTRANS': 53, 'TRANS': 930} Chain breaks: 8 Unresolved non-hydrogen bonds: 736 Unresolved non-hydrogen angles: 947 Unresolved non-hydrogen dihedrals: 605 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 15, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 445 Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 7080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7080 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 52, 'TRANS': 923} Chain breaks: 9 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 13, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 11, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 371 Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 273 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 15.59, per 1000 atoms: 0.67 Number of scatterers: 23123 At special positions: 0 Unit cell: (129.15, 133.35, 200.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4502 8.00 N 3858 7.00 C 14661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 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=2.09 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=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.08 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 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 C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.10 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.06 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.08 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.11 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 801 " Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 3.2 seconds 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 29.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.187A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.771A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.763A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) 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 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.085A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.889A 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 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.161A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'E' and resid 21 through 36 Processing helix chain 'E' and resid 41 through 55 removed outlier: 4.063A pdb=" N GLU E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.800A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 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 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.976A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.886A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.995A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.248A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'G' and resid 21 through 36 Processing helix chain 'G' and resid 41 through 55 removed outlier: 4.168A pdb=" N GLU G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.390A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.694A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.817A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.883A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.756A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 21 through 36 removed outlier: 3.852A pdb=" N LEU F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 55 removed outlier: 4.242A pdb=" N GLU F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.011A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.831A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.732A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.033A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.310A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.250A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.346A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.346A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.440A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.181A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.601A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.704A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.806A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.852A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.426A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.673A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.927A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.833A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.338A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.500A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.258A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.558A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.439A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.584A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.704A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.414A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 787 through 790 Processing sheet with id=AD7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.437A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.687A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.705A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.376A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.078A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.078A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.523A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.573A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.378A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.876A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.453A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.818A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3114 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: 12.17 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4955 1.32 - 1.46: 7470 1.46 - 1.59: 11018 1.59 - 1.73: 6 1.73 - 1.86: 126 Bond restraints: 23575 Sorted by residual: bond pdb=" N PRO C 600 " pdb=" CD PRO C 600 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.48e+01 bond pdb=" CB LEU C 242 " pdb=" CG LEU C 242 " ideal model delta sigma weight residual 1.530 1.614 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" CB LEU A 110 " pdb=" CG LEU A 110 " ideal model delta sigma weight residual 1.530 1.613 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CB LEU B 242 " pdb=" CG LEU B 242 " ideal model delta sigma weight residual 1.530 1.613 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB LEU C 916 " pdb=" CG LEU C 916 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 23570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 31786 4.63 - 9.25: 422 9.25 - 13.88: 6 13.88 - 18.50: 1 18.50 - 23.13: 5 Bond angle restraints: 32220 Sorted by residual: angle pdb=" CD1 LEU B 962 " pdb=" CG LEU B 962 " pdb=" CD2 LEU B 962 " ideal model delta sigma weight residual 110.80 133.93 -23.13 2.20e+00 2.07e-01 1.11e+02 angle pdb=" CD1 LEU C 916 " pdb=" CG LEU C 916 " pdb=" CD2 LEU C 916 " ideal model delta sigma weight residual 110.80 132.63 -21.83 2.20e+00 2.07e-01 9.85e+01 angle pdb=" CD1 LEU A 938 " pdb=" CG LEU A 938 " pdb=" CD2 LEU A 938 " ideal model delta sigma weight residual 110.80 132.25 -21.45 2.20e+00 2.07e-01 9.51e+01 angle pdb=" CD1 LEU B 966 " pdb=" CG LEU B 966 " pdb=" CD2 LEU B 966 " ideal model delta sigma weight residual 110.80 130.86 -20.06 2.20e+00 2.07e-01 8.31e+01 angle pdb=" CD1 LEU B1012 " pdb=" CG LEU B1012 " pdb=" CD2 LEU B1012 " ideal model delta sigma weight residual 110.80 92.22 18.58 2.20e+00 2.07e-01 7.13e+01 ... (remaining 32215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14219 18.00 - 35.99: 447 35.99 - 53.99: 76 53.99 - 71.98: 41 71.98 - 89.98: 14 Dihedral angle restraints: 14797 sinusoidal: 5802 harmonic: 8995 Sorted by residual: dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 151.05 -58.05 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 134.82 -41.82 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -50.88 -35.12 1 1.00e+01 1.00e-02 1.75e+01 ... (remaining 14794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 3741 0.208 - 0.416: 230 0.416 - 0.624: 4 0.624 - 0.833: 1 0.833 - 1.041: 1 Chirality restraints: 3977 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.08e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.56e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.36e+01 ... (remaining 3974 not shown) Planarity restraints: 4190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.053 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN C 331 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.083 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.045 2.00e-02 2.50e+03 4.52e-02 2.55e+01 pdb=" CG ASN C 234 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG C1301 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.041 2.00e-02 2.50e+03 4.36e-02 2.38e+01 pdb=" CG ASN B 709 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG B1309 " -0.053 2.00e-02 2.50e+03 ... (remaining 4187 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 7029 2.83 - 3.35: 20549 3.35 - 3.87: 38567 3.87 - 4.38: 44350 4.38 - 4.90: 73972 Nonbonded interactions: 184467 Sorted by model distance: nonbonded pdb=" ND2 ASN C 196 " pdb=" O ILE C 233 " model vdw 2.317 3.120 nonbonded pdb=" NZ LYS A 825 " pdb=" O LEU A 938 " model vdw 2.388 3.120 nonbonded pdb=" NZ LYS A1028 " pdb=" O PHE A1042 " model vdw 2.396 3.120 nonbonded pdb=" N SER B 813 " pdb=" N LYS B 814 " model vdw 2.398 2.560 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.407 3.120 ... (remaining 184462 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 27 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 93 or (resid 94 through 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 107 or ( \ resid 108 through 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 119 or (resid 120 and (name N or name CA or name C or name O \ or name CB )) or resid 121 through 135 or (resid 138 and (name N or name CA or \ name C or name O or name CB )) or resid 139 through 140 or resid 166 through 172 \ or (resid 188 through 190 and (name N or name CA or name C or name O or name CB \ )) or resid 191 through 204 or (resid 205 and (name N or name CA or name C or n \ ame O or name CB )) or resid 206 through 207 or (resid 208 and (name N or name C \ A or name C or name O or name CB )) or resid 209 or (resid 210 and (name N or na \ me CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 a \ nd (name N or name CA or name C or name O or name CB )) or resid 219 through 220 \ or (resid 221 through 222 and (name N or name CA or name C or name O or name CB \ )) or resid 223 through 227 or (resid 228 through 229 and (name N or name CA or \ name C or name O or name CB )) or resid 230 through 322 or (resid 323 through 3 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 325 through \ 331 or (resid 332 through 335 and (name N or name CA or name C or name O or nam \ e CB )) or resid 336 through 339 or (resid 340 through 342 and (name N or name C \ A or name C or name O or name CB )) or resid 343 through 346 or (resid 347 throu \ gh 352 and (name N or name CA or name C or name O or name CB )) or resid 353 thr \ ough 356 or (resid 357 and (name N or name CA or name C or name O or name CB )) \ or resid 358 or (resid 359 through 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 through 363 or (resid 364 through 378 and (name N o \ r name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (name \ N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 throu \ gh 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or \ (resid 385 through 390 and (name N or name CA or name C or name O or name CB )) \ or resid 391 through 397 or (resid 398 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 428 or (resid 429 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 445 and (n \ ame N or name CA or name C or name O or name CB )) or resid 446 through 447 or ( \ resid 448 through 462 and (name N or name CA or name C or name O or name CB )) o \ r resid 463 or (resid 464 through 475 and (name N or name CA or name C or name O \ or name CB )) or resid 476 through 488 or (resid 489 through 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 or (resid 492 through 49 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 496 or (resi \ d 497 through 498 and (name N or name CA or name C or name O or name CB )) or re \ sid 499 through 500 or (resid 501 and (name N or name CA or name C or name O or \ name CB )) or resid 502 or (resid 503 and (name N or name CA or name C or name O \ or name CB )) or resid 504 or (resid 505 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (na \ me N or name CA or name C or name O or name CB )) or resid 525 through 527 or (r \ esid 528 through 531 and (name N or name CA or name C or name O or name CB )) or \ resid 532 through 536 or (resid 537 and (name N or name CA or name C or name O \ or name CB )) or resid 538 through 553 or (resid 554 and (name N or name CA or n \ ame C or name O or name CB )) or resid 555 through 580 or (resid 581 and (name N \ or name CA or name C or name O or name CB )) or resid 582 or (resid 583 and (na \ me N or name CA or name C or name O or name CB )) or resid 584 through 653 or (r \ esid 654 and (name N or name CA or name C or name O or name CB )) or resid 655 t \ hrough 675 or (resid 676 and (name N or name CA or name C or name O or name CB ) \ ) or resid 690 through 701 or (resid 702 and (name N or name CA or name C or nam \ e O or name CB )) or resid 703 through 744 or (resid 745 through 746 and (name N \ or name CA or name C or name O or name CB )) or resid 747 or (resid 748 and (na \ me N or name CA or name C or name O or name CB )) or resid 749 or (resid 750 and \ (name N or name CA or name C or name O or name CB )) or resid 751 through 757 o \ r (resid 758 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 59 through 785 or (resid 786 and (name N or name CA or name C or name O or name \ CB )) or resid 787 through 793 or (resid 794 and (name N or name CA or name C or \ name O or name CB )) or resid 795 through 810 or (resid 811 and (name N or name \ CA or name C or name O or name CB )) or resid 812 through 813 or (resid 814 and \ (name N or name CA or name C or name O or name CB )) or resid 815 through 936 o \ r (resid 937 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 38 or (resid 939 through 941 and (name N or name CA or name C or name O or name \ CB )) or resid 942 through 973 or (resid 974 and (name N or name CA or name C or \ name O or name CB )) or resid 975 through 987 or (resid 988 through 989 and (na \ me N or name CA or name C or name O or name CB )) or resid 990 through 1044 or ( \ resid 1045 and (name N or name CA or name C or name O or name CB )) or resid 104 \ 6 through 1091 or (resid 1092 and (name N or name CA or name C or name O or name \ CB )) or resid 1093 through 1126 or (resid 1127 and (name N or name CA or name \ C or name O or name CB )) or resid 1128 through 1141 or (resid 1142 and (name N \ or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1145 through 1146 or \ (resid 1147 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 301 through 1311)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 86 or (resid 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 93 or (resi \ d 94 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 through 107 or (resid 108 through 110 and (name N or name CA or name C or \ name O or name CB )) or (resid 116 and (name N or name CA or name C or name O o \ r name CB )) or resid 117 through 119 or (resid 120 and (name N or name CA or na \ me C or name O or name CB )) or resid 121 through 125 or (resid 126 through 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 13 \ 1 or (resid 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or \ resid 135 or (resid 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 or (resid 140 and (name N or name CA or name C or name O or name C \ B )) or resid 166 or (resid 167 through 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 197 or (resid 198 and (name N or name \ CA or name C or name O or name CB )) or resid 199 through 204 or (resid 205 and \ (name N or name CA or name C or name O or name CB )) or resid 206 through 207 or \ (resid 208 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 9 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 228 or (resid 229 and (name N or name CA or name C or \ name O or name CB )) or resid 230 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 339 or (resid 340 through 342 and (name N or name CA or na \ me C or name O or name CB )) or resid 343 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 364 or (resid \ 365 through 378 and (name N or name CA or name C or name O or name CB )) or resi \ d 379 through 389 or (resid 390 and (name N or name CA or name C or name O or na \ me CB )) or resid 391 through 397 or (resid 398 through 403 and (name N or name \ CA or name C or name O or name CB )) or resid 404 through 417 or (resid 418 thro \ ugh 425 and (name N or name CA or name C or name O or name CB )) or resid 426 th \ rough 510 or (resid 511 through 524 and (name N or name CA or name C or name O o \ r name CB )) or resid 525 through 528 or (resid 529 through 531 and (name N or n \ ame CA or name C or name O or name CB )) or resid 532 through 536 or (resid 537 \ and (name N or name CA or name C or name O or name CB )) or resid 538 through 55 \ 5 or (resid 556 and (name N or name CA or name C or name O or name CB )) or resi \ d 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) or \ resid 559 through 580 or (resid 581 and (name N or name CA or name C or name O o \ r name CB )) or resid 582 through 645 or (resid 646 through 647 and (name N or n \ ame CA or name C or name O or name CB )) or resid 648 through 653 or (resid 654 \ and (name N or name CA or name C or name O or name CB )) or resid 655 through 74 \ 4 or (resid 745 through 746 and (name N or name CA or name C or name O or name C \ B )) or resid 747 or (resid 748 and (name N or name CA or name C or name O or na \ me CB )) or resid 749 or (resid 750 and (name N or name CA or name C or name O o \ r name CB )) or resid 751 through 757 or (resid 758 and (name N or name CA or na \ me C or name O or name CB )) or resid 759 through 809 or (resid 810 through 811 \ and (name N or name CA or name C or name O or name CB )) or resid 812 through 81 \ 3 or (resid 814 and (name N or name CA or name C or name O or name CB )) or resi \ d 815 through 826 or resid 856 through 936 or (resid 937 and (name N or name CA \ or name C or name O or name CB )) or resid 938 or (resid 939 through 941 and (na \ me N or name CA or name C or name O or name CB )) or resid 942 through 973 or (r \ esid 974 and (name N or name CA or name C or name O or name CB )) or resid 975 t \ hrough 984 or (resid 985 and (name N or name CA or name C or name O or name CB ) \ ) or resid 986 through 987 or (resid 988 through 989 and (name N or name CA or n \ ame C or name O or name CB )) or resid 990 through 1044 or (resid 1045 and (name \ N or name CA or name C or name O or name CB )) or resid 1046 through 1126 or (r \ esid 1127 and (name N or name CA or name C or name O or name CB )) or resid 1128 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 through 1147 or resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 110 or resid 116 through 126 or (resid 127 thro \ ugh 129 and (name N or name CA or name C or name O or name CB )) or resid 130 th \ rough 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) \ or resid 133 through 135 or resid 138 through 140 or resid 166 through 172 or ( \ resid 188 through 190 and (name N or name CA or name C or name O or name CB )) o \ r resid 191 through 210 or resid 216 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 227 or \ (resid 228 through 229 and (name N or name CA or name C or name O or name CB )) \ or resid 230 through 236 or (resid 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 through 346 or (resid 347 through 352 and (name N o \ r name CA or name C or name O or name CB )) or resid 353 through 373 or (resid 3 \ 74 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 through 393 or (resid 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 515 or resid 522 through 553 or (resid 554 and (nam \ e N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 and \ (name N or name CA or name C or name O or name CB )) or resid 557 or (resid 558 \ and (name N or name CA or name C or name O or name CB )) or resid 559 through 56 \ 7 or (resid 568 and (name N or name CA or name C or name O or name CB )) or resi \ d 569 through 645 or (resid 646 through 647 and (name N or name CA or name C or \ name O or name CB )) or resid 648 through 675 or (resid 676 and (name N or name \ CA or name C or name O or name CB )) or resid 690 through 701 or (resid 702 and \ (name N or name CA or name C or name O or name CB )) or resid 703 through 793 or \ (resid 794 and (name N or name CA or name C or name O or name CB )) or resid 79 \ 5 through 809 or (resid 810 through 811 and (name N or name CA or name C or name \ O or name CB )) or resid 812 or (resid 813 through 814 and (name N or name CA o \ r name C or name O or name CB )) or resid 815 through 826 or resid 856 through 9 \ 84 or (resid 985 and (name N or name CA or name C or name O or name CB )) or res \ id 986 through 1143 or (resid 1144 and (name N or name CA or name C or name O or \ name CB )) or resid 1145 through 1146 or (resid 1147 and (name N or name CA or \ name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 9.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.250 Set scattering table: 0.210 Process input model: 61.840 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:19.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.014 0.125 23673 Z= 0.778 Angle : 1.468 35.511 32475 Z= 0.963 Chirality : 0.100 1.041 3977 Planarity : 0.005 0.024 4144 Dihedral : 9.945 89.979 8856 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 0.93 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3039 helix: 0.31 (0.17), residues: 810 sheet: 0.90 (0.19), residues: 631 loop : 0.16 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP C1102 HIS 0.005 0.001 HIS A1083 PHE 0.028 0.004 PHE A 898 TYR 0.046 0.005 TYR A 495 ARG 0.006 0.001 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.06757 ( 46) link_NAG-ASN : angle 4.30186 ( 138) link_BETA1-4 : bond 0.06837 ( 13) link_BETA1-4 : angle 3.68947 ( 39) hydrogen bonds : bond 0.16212 ( 1133) hydrogen bonds : angle 8.07830 ( 3114) SS BOND : bond 0.02950 ( 39) SS BOND : angle 2.54517 ( 78) covalent geometry : bond 0.01403 (23575) covalent geometry : angle 1.43521 (32220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 463 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.7654 (ttt) cc_final: 0.7386 (ttm) REVERT: C 756 TYR cc_start: 0.7962 (m-80) cc_final: 0.7733 (m-80) REVERT: C 902 MET cc_start: 0.8493 (mmp) cc_final: 0.8280 (mmp) REVERT: B 725 GLU cc_start: 0.7557 (tt0) cc_final: 0.7326 (tt0) REVERT: B 1029 MET cc_start: 0.9064 (tpp) cc_final: 0.8659 (tpp) outliers start: 13 outliers final: 2 residues processed: 476 average time/residue: 1.2844 time to fit residues: 705.9673 Evaluate side-chains 237 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 235 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 179 optimal weight: 0.6980 chunk 279 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 965 GLN A1125 ASN C 207 HIS C 784 GLN C 965 GLN C1005 GLN B 115 GLN B 196 ASN B 544 ASN B 580 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1071 GLN B1135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3857 r_free = 0.3857 target = 0.150389 restraints weight = 29078.586| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.70 r_work: 0.3629 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23673 Z= 0.161 Angle : 0.661 14.494 32475 Z= 0.339 Chirality : 0.049 0.854 3977 Planarity : 0.004 0.039 4144 Dihedral : 5.506 58.848 4485 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.35 % Favored : 98.62 % Rotamer: Outliers : 2.15 % Allowed : 10.18 % Favored : 87.67 % 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: 0.93 (0.14), residues: 3039 helix: 1.84 (0.18), residues: 804 sheet: 0.63 (0.18), residues: 666 loop : 0.04 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.008 0.001 HIS A 655 PHE 0.024 0.002 PHE B 32 TYR 0.028 0.002 TYR A 495 ARG 0.006 0.001 ARG A1091 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 46) link_NAG-ASN : angle 3.49767 ( 138) link_BETA1-4 : bond 0.00791 ( 13) link_BETA1-4 : angle 2.27478 ( 39) hydrogen bonds : bond 0.05206 ( 1133) hydrogen bonds : angle 6.07526 ( 3114) SS BOND : bond 0.00344 ( 39) SS BOND : angle 1.00205 ( 78) covalent geometry : bond 0.00351 (23575) covalent geometry : angle 0.61614 (32220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 2.398 Fit side-chains revert: symmetry clash REVERT: A 242 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6405 (mt) REVERT: A 378 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7652 (mmmt) REVERT: C 206 LYS cc_start: 0.7424 (tptt) cc_final: 0.7011 (tppp) REVERT: C 207 HIS cc_start: 0.6993 (m170) cc_final: 0.6758 (m-70) REVERT: C 237 ARG cc_start: 0.7483 (mtm110) cc_final: 0.6484 (ptm-80) REVERT: C 756 TYR cc_start: 0.8502 (m-80) cc_final: 0.8117 (m-80) REVERT: C 760 CYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6575 (t) REVERT: C 990 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: B 191 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6622 (mm-30) REVERT: B 206 LYS cc_start: 0.8397 (tptt) cc_final: 0.7835 (tttm) REVERT: B 661 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: B 725 GLU cc_start: 0.8271 (tt0) cc_final: 0.8032 (tt0) REVERT: B 947 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7976 (mmtm) REVERT: B 964 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8117 (tptt) REVERT: B 994 ASP cc_start: 0.7872 (t70) cc_final: 0.7637 (t70) REVERT: B 1029 MET cc_start: 0.9152 (tpp) cc_final: 0.8820 (tpp) outliers start: 46 outliers final: 18 residues processed: 289 average time/residue: 1.2016 time to fit residues: 407.8313 Evaluate side-chains 240 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 299 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 266 optimal weight: 0.9990 chunk 272 optimal weight: 0.5980 chunk 205 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 334 ASN A 544 ASN A 675 GLN A 804 GLN A 913 GLN A 935 GLN A 955 ASN A1011 GLN A1071 GLN A1125 ASN C 935 GLN C 955 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.198113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.154744 restraints weight = 29191.714| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.63 r_work: 0.3641 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23673 Z= 0.211 Angle : 0.652 13.353 32475 Z= 0.332 Chirality : 0.048 0.464 3977 Planarity : 0.005 0.057 4144 Dihedral : 5.039 59.444 4483 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.93 % Rotamer: Outliers : 3.74 % Allowed : 9.67 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3039 helix: 2.00 (0.19), residues: 796 sheet: 0.32 (0.18), residues: 702 loop : -0.25 (0.15), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.007 0.002 HIS A 655 PHE 0.026 0.002 PHE B 133 TYR 0.026 0.002 TYR C1067 ARG 0.006 0.001 ARG C 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00841 ( 46) link_NAG-ASN : angle 3.23275 ( 138) link_BETA1-4 : bond 0.00555 ( 13) link_BETA1-4 : angle 2.03904 ( 39) hydrogen bonds : bond 0.04789 ( 1133) hydrogen bonds : angle 5.70436 ( 3114) SS BOND : bond 0.00384 ( 39) SS BOND : angle 1.41322 ( 78) covalent geometry : bond 0.00494 (23575) covalent geometry : angle 0.61100 (32220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 242 time to evaluate : 2.622 Fit side-chains REVERT: A 242 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6465 (mt) REVERT: A 309 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: A 357 ARG cc_start: 0.7456 (tpt-90) cc_final: 0.7249 (ttm-80) REVERT: A 360 ASN cc_start: 0.7466 (m-40) cc_final: 0.7135 (p0) REVERT: A 378 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7841 (mmmt) REVERT: A 505 TYR cc_start: 0.6137 (m-80) cc_final: 0.5907 (m-10) REVERT: A 750 SER cc_start: 0.8220 (t) cc_final: 0.7987 (m) REVERT: A 786 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7103 (mttp) REVERT: A 868 GLU cc_start: 0.8047 (tt0) cc_final: 0.7487 (mp0) REVERT: A 1113 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: A 1142 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7573 (tp40) REVERT: C 190 ARG cc_start: 0.5774 (OUTLIER) cc_final: 0.4556 (mmm-85) REVERT: C 207 HIS cc_start: 0.6488 (m170) cc_final: 0.6184 (m-70) REVERT: C 237 ARG cc_start: 0.7491 (mtm110) cc_final: 0.6710 (ptm-80) REVERT: C 314 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: C 319 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7775 (ttt-90) REVERT: C 613 GLN cc_start: 0.8749 (mt0) cc_final: 0.8342 (mt0) REVERT: C 756 TYR cc_start: 0.8680 (m-80) cc_final: 0.8265 (m-80) REVERT: C 821 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7713 (tm) REVERT: C 990 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: C 1017 GLU cc_start: 0.8470 (tt0) cc_final: 0.8083 (tt0) REVERT: B 191 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 725 GLU cc_start: 0.8280 (tt0) cc_final: 0.8010 (tt0) REVERT: B 787 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: B 918 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 964 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8227 (tptt) REVERT: B 1029 MET cc_start: 0.9143 (tpp) cc_final: 0.8773 (tpp) outliers start: 80 outliers final: 31 residues processed: 294 average time/residue: 1.1146 time to fit residues: 383.8410 Evaluate side-chains 256 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 121 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 294 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1119 ASN A1125 ASN C 580 GLN B 66 HIS B 658 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143605 restraints weight = 28984.707| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.21 r_work: 0.3544 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23673 Z= 0.152 Angle : 0.581 12.731 32475 Z= 0.293 Chirality : 0.046 0.420 3977 Planarity : 0.004 0.045 4144 Dihedral : 4.661 44.732 4482 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 3.55 % Allowed : 10.46 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3039 helix: 2.17 (0.19), residues: 799 sheet: 0.32 (0.18), residues: 667 loop : -0.27 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.004 0.001 HIS A 655 PHE 0.019 0.002 PHE B 541 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 46) link_NAG-ASN : angle 3.02239 ( 138) link_BETA1-4 : bond 0.00520 ( 13) link_BETA1-4 : angle 1.75989 ( 39) hydrogen bonds : bond 0.04164 ( 1133) hydrogen bonds : angle 5.48974 ( 3114) SS BOND : bond 0.00527 ( 39) SS BOND : angle 1.22330 ( 78) covalent geometry : bond 0.00346 (23575) covalent geometry : angle 0.54203 (32220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 239 time to evaluate : 2.550 Fit side-chains REVERT: A 52 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: A 242 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6510 (mt) REVERT: A 309 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: A 357 ARG cc_start: 0.7560 (tpt-90) cc_final: 0.7315 (ttm-80) REVERT: A 360 ASN cc_start: 0.7558 (m-40) cc_final: 0.7164 (p0) REVERT: A 505 TYR cc_start: 0.6236 (m-80) cc_final: 0.5954 (m-10) REVERT: A 553 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8525 (m) REVERT: A 697 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8691 (ptm) REVERT: A 786 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7174 (mttp) REVERT: A 868 GLU cc_start: 0.8242 (tt0) cc_final: 0.7572 (mp0) REVERT: A 1113 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: C 190 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.4755 (mmm-85) REVERT: C 207 HIS cc_start: 0.6534 (m170) cc_final: 0.6196 (m-70) REVERT: C 319 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7918 (ttt180) REVERT: C 574 ASP cc_start: 0.7545 (p0) cc_final: 0.7252 (p0) REVERT: C 613 GLN cc_start: 0.8862 (mt0) cc_final: 0.8531 (mt0) REVERT: C 756 TYR cc_start: 0.8718 (m-80) cc_final: 0.8275 (m-80) REVERT: C 821 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7849 (tm) REVERT: C 990 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: C 1017 GLU cc_start: 0.8684 (tt0) cc_final: 0.8370 (tt0) REVERT: B 52 GLN cc_start: 0.8043 (pt0) cc_final: 0.7736 (tt0) REVERT: B 54 LEU cc_start: 0.8266 (mm) cc_final: 0.8064 (mp) REVERT: B 191 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7131 (mt-10) REVERT: B 654 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: B 661 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: B 725 GLU cc_start: 0.8473 (tt0) cc_final: 0.8196 (tt0) REVERT: B 787 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: B 918 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: B 964 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8309 (tptt) REVERT: B 988 GLU cc_start: 0.7734 (mp0) cc_final: 0.7518 (mm-30) REVERT: B 1029 MET cc_start: 0.9109 (tpp) cc_final: 0.8726 (tpp) outliers start: 76 outliers final: 33 residues processed: 284 average time/residue: 1.1666 time to fit residues: 387.0351 Evaluate side-chains 257 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 173 optimal weight: 0.8980 chunk 227 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 268 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1119 ASN B 66 HIS B 544 ASN B 804 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.197122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147067 restraints weight = 29035.207| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.83 r_work: 0.3564 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23673 Z= 0.163 Angle : 0.593 13.259 32475 Z= 0.296 Chirality : 0.046 0.390 3977 Planarity : 0.004 0.042 4144 Dihedral : 4.754 54.279 4482 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % Rotamer: Outliers : 3.50 % Allowed : 11.49 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3039 helix: 2.19 (0.19), residues: 798 sheet: 0.34 (0.19), residues: 645 loop : -0.29 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.004 0.001 HIS A 655 PHE 0.021 0.002 PHE B 541 TYR 0.021 0.002 TYR C1067 ARG 0.008 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00798 ( 46) link_NAG-ASN : angle 3.28776 ( 138) link_BETA1-4 : bond 0.00471 ( 13) link_BETA1-4 : angle 1.67604 ( 39) hydrogen bonds : bond 0.04176 ( 1133) hydrogen bonds : angle 5.41585 ( 3114) SS BOND : bond 0.00218 ( 39) SS BOND : angle 1.57622 ( 78) covalent geometry : bond 0.00378 (23575) covalent geometry : angle 0.54700 (32220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 5.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: A 242 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6265 (mt) REVERT: A 287 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7949 (t70) REVERT: A 309 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: A 324 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: A 360 ASN cc_start: 0.7502 (m-40) cc_final: 0.7087 (p0) REVERT: A 505 TYR cc_start: 0.6130 (m-80) cc_final: 0.5768 (m-10) REVERT: A 786 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7176 (mttp) REVERT: A 868 GLU cc_start: 0.8093 (tt0) cc_final: 0.7334 (mp0) REVERT: A 1113 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: C 190 ARG cc_start: 0.5802 (OUTLIER) cc_final: 0.4619 (mmm-85) REVERT: C 207 HIS cc_start: 0.6506 (m170) cc_final: 0.6109 (m-70) REVERT: C 319 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7754 (ttt180) REVERT: C 327 VAL cc_start: 0.7244 (t) cc_final: 0.7022 (p) REVERT: C 574 ASP cc_start: 0.7294 (p0) cc_final: 0.6948 (p0) REVERT: C 613 GLN cc_start: 0.8743 (mt0) cc_final: 0.8539 (mt0) REVERT: C 756 TYR cc_start: 0.8611 (m-80) cc_final: 0.8108 (m-80) REVERT: C 821 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7638 (tm) REVERT: C 990 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: C 1017 GLU cc_start: 0.8534 (tt0) cc_final: 0.8163 (tt0) REVERT: B 191 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6926 (mt-10) REVERT: B 200 TYR cc_start: 0.7042 (m-80) cc_final: 0.6689 (m-80) REVERT: B 309 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: B 654 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: B 661 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: B 725 GLU cc_start: 0.8359 (tt0) cc_final: 0.8077 (tt0) REVERT: B 787 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: B 918 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: B 988 GLU cc_start: 0.7667 (mp0) cc_final: 0.7349 (mm-30) outliers start: 75 outliers final: 41 residues processed: 278 average time/residue: 1.3340 time to fit residues: 436.9288 Evaluate side-chains 272 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 72 optimal weight: 0.5980 chunk 247 optimal weight: 20.0000 chunk 146 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 190 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 297 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 196 ASN C 955 ASN B 66 HIS B 544 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.197846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143858 restraints weight = 28780.710| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.15 r_work: 0.3559 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23673 Z= 0.136 Angle : 0.562 14.382 32475 Z= 0.281 Chirality : 0.045 0.367 3977 Planarity : 0.004 0.039 4144 Dihedral : 4.633 57.212 4482 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 3.27 % Allowed : 12.42 % Favored : 84.31 % 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: 0.78 (0.15), residues: 3039 helix: 2.27 (0.19), residues: 801 sheet: 0.35 (0.19), residues: 639 loop : -0.28 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 PHE 0.023 0.001 PHE B 541 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 46) link_NAG-ASN : angle 3.17328 ( 138) link_BETA1-4 : bond 0.00474 ( 13) link_BETA1-4 : angle 1.56215 ( 39) hydrogen bonds : bond 0.03908 ( 1133) hydrogen bonds : angle 5.29253 ( 3114) SS BOND : bond 0.00200 ( 39) SS BOND : angle 1.17075 ( 78) covalent geometry : bond 0.00311 (23575) covalent geometry : angle 0.51812 (32220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8656 (tt0) cc_final: 0.8155 (tt0) REVERT: A 242 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6416 (mt) REVERT: A 287 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7887 (t70) REVERT: A 309 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: A 324 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: A 360 ASN cc_start: 0.7545 (m-40) cc_final: 0.7155 (p0) REVERT: A 505 TYR cc_start: 0.6197 (m-80) cc_final: 0.5859 (m-10) REVERT: A 553 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8466 (m) REVERT: C 190 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.4970 (mmm-85) REVERT: C 202 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6900 (mptt) REVERT: C 207 HIS cc_start: 0.6565 (m170) cc_final: 0.6198 (m-70) REVERT: C 319 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7798 (ttt180) REVERT: C 574 ASP cc_start: 0.7541 (p0) cc_final: 0.7246 (p0) REVERT: C 613 GLN cc_start: 0.8832 (mt0) cc_final: 0.8548 (mt0) REVERT: C 756 TYR cc_start: 0.8694 (m-80) cc_final: 0.8254 (m-80) REVERT: C 821 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7877 (tm) REVERT: C 983 ARG cc_start: 0.7411 (ttm170) cc_final: 0.7099 (mtm-85) REVERT: C 990 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: C 1017 GLU cc_start: 0.8661 (tt0) cc_final: 0.8364 (tt0) REVERT: B 200 TYR cc_start: 0.7122 (m-80) cc_final: 0.6852 (m-80) REVERT: B 654 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: B 725 GLU cc_start: 0.8508 (tt0) cc_final: 0.8230 (tt0) REVERT: B 918 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: B 988 GLU cc_start: 0.7767 (mp0) cc_final: 0.7504 (mm-30) outliers start: 70 outliers final: 34 residues processed: 257 average time/residue: 1.1315 time to fit residues: 342.1376 Evaluate side-chains 250 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 41 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 116 optimal weight: 0.0370 chunk 220 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 134 optimal weight: 50.0000 chunk 128 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN C 196 ASN C 690 GLN B 66 HIS B 935 GLN B 955 ASN B1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143245 restraints weight = 28991.468| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.20 r_work: 0.3547 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23673 Z= 0.135 Angle : 0.562 13.251 32475 Z= 0.279 Chirality : 0.045 0.346 3977 Planarity : 0.004 0.041 4144 Dihedral : 4.534 59.547 4482 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.97 % Favored : 97.93 % Rotamer: Outliers : 3.13 % Allowed : 12.80 % Favored : 84.07 % 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: 0.77 (0.15), residues: 3039 helix: 2.32 (0.19), residues: 799 sheet: 0.34 (0.19), residues: 650 loop : -0.32 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 PHE 0.026 0.001 PHE B 541 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00630 ( 46) link_NAG-ASN : angle 3.07912 ( 138) link_BETA1-4 : bond 0.00483 ( 13) link_BETA1-4 : angle 1.49820 ( 39) hydrogen bonds : bond 0.03834 ( 1133) hydrogen bonds : angle 5.23783 ( 3114) SS BOND : bond 0.00238 ( 39) SS BOND : angle 1.58919 ( 78) covalent geometry : bond 0.00309 (23575) covalent geometry : angle 0.51820 (32220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8665 (tt0) cc_final: 0.8166 (tt0) REVERT: A 242 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6336 (mt) REVERT: A 287 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7730 (t70) REVERT: A 309 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: A 324 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: A 360 ASN cc_start: 0.7582 (m-40) cc_final: 0.7206 (p0) REVERT: A 505 TYR cc_start: 0.6204 (m-80) cc_final: 0.5856 (m-10) REVERT: A 553 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8365 (m) REVERT: A 786 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7175 (mttp) REVERT: A 1113 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8128 (mt0) REVERT: C 190 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.4951 (mmm-85) REVERT: C 202 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6859 (mptt) REVERT: C 207 HIS cc_start: 0.6664 (m170) cc_final: 0.6308 (m-70) REVERT: C 237 ARG cc_start: 0.7479 (mtm110) cc_final: 0.6679 (ptm-80) REVERT: C 319 ARG cc_start: 0.8079 (ttm110) cc_final: 0.7778 (ttt180) REVERT: C 532 ASN cc_start: 0.6373 (t0) cc_final: 0.6094 (m-40) REVERT: C 544 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7545 (m110) REVERT: C 613 GLN cc_start: 0.8773 (mt0) cc_final: 0.8506 (mt0) REVERT: C 756 TYR cc_start: 0.8677 (m-80) cc_final: 0.8241 (m-80) REVERT: C 821 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7862 (tm) REVERT: C 990 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: C 1002 GLN cc_start: 0.8491 (tt0) cc_final: 0.8259 (tm-30) REVERT: C 1017 GLU cc_start: 0.8656 (tt0) cc_final: 0.8360 (tt0) REVERT: B 191 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6647 (mm-30) REVERT: B 200 TYR cc_start: 0.7071 (m-80) cc_final: 0.6731 (m-80) REVERT: B 309 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: B 654 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: B 725 GLU cc_start: 0.8503 (tt0) cc_final: 0.8217 (tt0) REVERT: B 787 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: B 918 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: B 988 GLU cc_start: 0.7788 (mp0) cc_final: 0.7453 (mm-30) outliers start: 67 outliers final: 38 residues processed: 262 average time/residue: 1.1997 time to fit residues: 369.4945 Evaluate side-chains 263 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN C 196 ASN B 30 ASN B 544 ASN B 613 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144830 restraints weight = 28842.930| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.35 r_work: 0.3559 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23673 Z= 0.174 Angle : 0.590 13.036 32475 Z= 0.293 Chirality : 0.046 0.424 3977 Planarity : 0.004 0.038 4144 Dihedral : 4.629 56.114 4482 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.63 % Rotamer: Outliers : 3.13 % Allowed : 13.08 % Favored : 83.79 % 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 (0.15), residues: 3039 helix: 2.28 (0.19), residues: 800 sheet: 0.26 (0.19), residues: 665 loop : -0.35 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 64 HIS 0.006 0.001 HIS B 655 PHE 0.026 0.002 PHE B 541 TYR 0.022 0.002 TYR C1067 ARG 0.005 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00638 ( 46) link_NAG-ASN : angle 3.28968 ( 138) link_BETA1-4 : bond 0.00430 ( 13) link_BETA1-4 : angle 1.50180 ( 39) hydrogen bonds : bond 0.04112 ( 1133) hydrogen bonds : angle 5.29189 ( 3114) SS BOND : bond 0.00211 ( 39) SS BOND : angle 1.17516 ( 78) covalent geometry : bond 0.00408 (23575) covalent geometry : angle 0.54676 (32220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 220 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8626 (tt0) cc_final: 0.8152 (tt0) REVERT: A 242 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6387 (mt) REVERT: A 309 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: A 324 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: A 360 ASN cc_start: 0.7575 (m-40) cc_final: 0.7204 (p0) REVERT: A 505 TYR cc_start: 0.6221 (m-80) cc_final: 0.5969 (m-10) REVERT: A 553 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8404 (m) REVERT: A 786 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7147 (mttp) REVERT: A 1113 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: C 190 ARG cc_start: 0.6123 (OUTLIER) cc_final: 0.4973 (mmm-85) REVERT: C 202 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6854 (mptt) REVERT: C 207 HIS cc_start: 0.6619 (m170) cc_final: 0.6322 (m-70) REVERT: C 532 ASN cc_start: 0.6463 (t0) cc_final: 0.6144 (m-40) REVERT: C 544 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7606 (m110) REVERT: C 568 ASP cc_start: 0.7138 (m-30) cc_final: 0.6878 (p0) REVERT: C 574 ASP cc_start: 0.7395 (p0) cc_final: 0.7089 (p0) REVERT: C 613 GLN cc_start: 0.8786 (mt0) cc_final: 0.8519 (mt0) REVERT: C 756 TYR cc_start: 0.8635 (m-80) cc_final: 0.8308 (m-80) REVERT: C 990 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: C 1017 GLU cc_start: 0.8566 (tt0) cc_final: 0.8270 (tt0) REVERT: B 54 LEU cc_start: 0.8287 (mm) cc_final: 0.8070 (mp) REVERT: B 191 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6770 (mm-30) REVERT: B 200 TYR cc_start: 0.7033 (m-80) cc_final: 0.6732 (m-80) REVERT: B 309 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: B 310 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: B 725 GLU cc_start: 0.8424 (tt0) cc_final: 0.8133 (tt0) REVERT: B 787 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: B 918 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: B 988 GLU cc_start: 0.7736 (mp0) cc_final: 0.7453 (mm-30) REVERT: B 1029 MET cc_start: 0.9117 (tpp) cc_final: 0.8762 (tpp) outliers start: 67 outliers final: 39 residues processed: 259 average time/residue: 1.1388 time to fit residues: 346.4213 Evaluate side-chains 263 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 235 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 141 optimal weight: 50.0000 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.197005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144635 restraints weight = 28899.257| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.51 r_work: 0.3544 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23673 Z= 0.169 Angle : 0.584 12.958 32475 Z= 0.291 Chirality : 0.046 0.340 3977 Planarity : 0.004 0.037 4144 Dihedral : 4.605 45.771 4482 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.24 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 13.97 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3039 helix: 2.33 (0.19), residues: 793 sheet: 0.27 (0.19), residues: 655 loop : -0.40 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1102 HIS 0.003 0.001 HIS A 655 PHE 0.025 0.002 PHE B 541 TYR 0.020 0.002 TYR C1067 ARG 0.009 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 46) link_NAG-ASN : angle 3.06653 ( 138) link_BETA1-4 : bond 0.00445 ( 13) link_BETA1-4 : angle 1.44883 ( 39) hydrogen bonds : bond 0.04048 ( 1133) hydrogen bonds : angle 5.26908 ( 3114) SS BOND : bond 0.00194 ( 39) SS BOND : angle 1.15488 ( 78) covalent geometry : bond 0.00397 (23575) covalent geometry : angle 0.54562 (32220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8648 (tt0) cc_final: 0.8186 (tt0) REVERT: A 242 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6295 (mt) REVERT: A 309 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6917 (tm-30) REVERT: A 324 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: A 360 ASN cc_start: 0.7608 (m-40) cc_final: 0.7210 (p0) REVERT: A 505 TYR cc_start: 0.6289 (m-80) cc_final: 0.5998 (m-80) REVERT: A 786 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7173 (mttp) REVERT: A 1113 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: C 190 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.4902 (mmm-85) REVERT: C 196 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6988 (m110) REVERT: C 202 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6790 (mptt) REVERT: C 206 LYS cc_start: 0.7722 (tptt) cc_final: 0.7446 (tppp) REVERT: C 207 HIS cc_start: 0.6547 (m170) cc_final: 0.6193 (m-70) REVERT: C 237 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6410 (ptm-80) REVERT: C 319 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7871 (ttt-90) REVERT: C 532 ASN cc_start: 0.6602 (t0) cc_final: 0.6263 (m-40) REVERT: C 568 ASP cc_start: 0.7086 (m-30) cc_final: 0.6301 (p0) REVERT: C 613 GLN cc_start: 0.8768 (mt0) cc_final: 0.8499 (mt0) REVERT: C 756 TYR cc_start: 0.8597 (m-80) cc_final: 0.8305 (m-80) REVERT: C 821 LEU cc_start: 0.8779 (tm) cc_final: 0.8574 (tt) REVERT: C 990 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: C 1017 GLU cc_start: 0.8542 (tt0) cc_final: 0.8256 (tt0) REVERT: B 52 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 191 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6780 (mm-30) REVERT: B 200 TYR cc_start: 0.6987 (m-80) cc_final: 0.6727 (m-80) REVERT: B 309 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: B 310 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8446 (ttmm) REVERT: B 591 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7346 (t) REVERT: B 661 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: B 725 GLU cc_start: 0.8443 (tt0) cc_final: 0.8179 (tt0) REVERT: B 787 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: B 918 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: B 988 GLU cc_start: 0.7754 (mp0) cc_final: 0.7409 (mm-30) REVERT: B 1029 MET cc_start: 0.9119 (tpp) cc_final: 0.8764 (tpp) outliers start: 59 outliers final: 34 residues processed: 251 average time/residue: 1.0696 time to fit residues: 316.2771 Evaluate side-chains 257 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.5980 chunk 157 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 210 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.197414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144232 restraints weight = 28778.158| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.25 r_work: 0.3531 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23673 Z= 0.149 Angle : 0.574 12.889 32475 Z= 0.286 Chirality : 0.045 0.338 3977 Planarity : 0.004 0.060 4144 Dihedral : 4.524 38.211 4482 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.11 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 14.11 % Favored : 83.42 % 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: 0.70 (0.15), residues: 3039 helix: 2.31 (0.19), residues: 807 sheet: 0.28 (0.19), residues: 653 loop : -0.41 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.026 0.002 PHE B 541 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 46) link_NAG-ASN : angle 3.03039 ( 138) link_BETA1-4 : bond 0.00439 ( 13) link_BETA1-4 : angle 1.40737 ( 39) hydrogen bonds : bond 0.03924 ( 1133) hydrogen bonds : angle 5.23827 ( 3114) SS BOND : bond 0.00172 ( 39) SS BOND : angle 1.21221 ( 78) covalent geometry : bond 0.00347 (23575) covalent geometry : angle 0.53576 (32220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6078 Ramachandran restraints generated. 3039 Oldfield, 0 Emsley, 3039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8691 (tt0) cc_final: 0.8234 (tt0) REVERT: A 242 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6278 (mt) REVERT: A 309 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: A 324 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: A 360 ASN cc_start: 0.7584 (m-40) cc_final: 0.7216 (p0) REVERT: A 505 TYR cc_start: 0.6308 (m-80) cc_final: 0.5985 (m-80) REVERT: A 786 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7193 (mttp) REVERT: A 1113 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: C 190 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5016 (mmm-85) REVERT: C 202 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6823 (mptt) REVERT: C 206 LYS cc_start: 0.7799 (tptt) cc_final: 0.7514 (tppp) REVERT: C 207 HIS cc_start: 0.6563 (m170) cc_final: 0.6199 (m-70) REVERT: C 224 GLU cc_start: 0.7425 (mp0) cc_final: 0.7198 (mp0) REVERT: C 237 ARG cc_start: 0.7458 (mtm110) cc_final: 0.6464 (ptm-80) REVERT: C 319 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7794 (ttt-90) REVERT: C 532 ASN cc_start: 0.6554 (t0) cc_final: 0.6223 (m-40) REVERT: C 544 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7700 (m110) REVERT: C 613 GLN cc_start: 0.8833 (mt0) cc_final: 0.8510 (mt0) REVERT: C 756 TYR cc_start: 0.8653 (m-80) cc_final: 0.8353 (m-80) REVERT: C 990 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: C 1017 GLU cc_start: 0.8664 (tt0) cc_final: 0.8374 (tt0) REVERT: B 191 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6858 (mm-30) REVERT: B 200 TYR cc_start: 0.7043 (m-80) cc_final: 0.6783 (m-80) REVERT: B 309 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7664 (mt-10) REVERT: B 310 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8448 (ttmm) REVERT: B 591 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7284 (t) REVERT: B 661 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: B 725 GLU cc_start: 0.8546 (tt0) cc_final: 0.8282 (tt0) REVERT: B 787 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: B 918 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: B 988 GLU cc_start: 0.7885 (mp0) cc_final: 0.7455 (mm-30) REVERT: B 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.8765 (tpp) outliers start: 53 outliers final: 33 residues processed: 242 average time/residue: 1.5489 time to fit residues: 449.8187 Evaluate side-chains 256 residues out of total 2733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 825 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 77 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 chunk 225 optimal weight: 0.0070 chunk 134 optimal weight: 40.0000 chunk 112 optimal weight: 0.0010 chunk 135 optimal weight: 50.0000 chunk 45 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 chunk 266 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 168 optimal weight: 0.0010 overall best weight: 0.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1125 ASN B 66 HIS B 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.199409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.155441 restraints weight = 29101.054| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.64 r_work: 0.3693 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23673 Z= 0.096 Angle : 0.527 12.565 32475 Z= 0.261 Chirality : 0.044 0.323 3977 Planarity : 0.004 0.060 4144 Dihedral : 4.163 39.385 4482 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.68 % Favored : 98.26 % Rotamer: Outliers : 1.68 % Allowed : 14.81 % Favored : 83.51 % 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: 0.85 (0.15), residues: 3039 helix: 2.47 (0.19), residues: 810 sheet: 0.31 (0.19), residues: 649 loop : -0.31 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A1048 PHE 0.027 0.001 PHE B 541 TYR 0.018 0.001 TYR A1138 ARG 0.006 0.000 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 46) link_NAG-ASN : angle 2.83225 ( 138) link_BETA1-4 : bond 0.00488 ( 13) link_BETA1-4 : angle 1.28787 ( 39) hydrogen bonds : bond 0.03322 ( 1133) hydrogen bonds : angle 5.01820 ( 3114) SS BOND : bond 0.00173 ( 39) SS BOND : angle 1.01205 ( 78) covalent geometry : bond 0.00208 (23575) covalent geometry : angle 0.49109 (32220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23599.17 seconds wall clock time: 410 minutes 54.64 seconds (24654.64 seconds total)