Starting phenix.real_space_refine on Thu Mar 5 12:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kdl_22826/03_2026/7kdl_22826.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 96 5.16 5 C 14244 2.51 5 N 3683 2.21 5 O 4342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7394 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 45, 'TRANS': 920} Chain breaks: 12 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 6863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6863 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 44, 'TRANS': 904} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7282 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 45, 'TRANS': 914} Chain breaks: 11 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 140 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.49, per 1000 atoms: 0.25 Number of scatterers: 22365 At special positions: 0 Unit cell: (137.54, 129.076, 177.744, 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 96 16.00 O 4342 8.00 N 3683 7.00 C 14244 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 717 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C 801 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 961.1 milliseconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5398 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 43 sheets defined 28.4% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 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 364 through 370 removed outlier: 3.927A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.558A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A 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 439 through 442 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.712A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.767A 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: 3.695A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.354A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.650A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.678A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.579A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.611A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.123A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.349A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.709A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.526A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.529A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.668A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.354A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.052A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.476A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.221A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.928A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.772A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 5.968A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.610A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.504A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.645A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.659A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.899A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.706A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.378A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.882A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.584A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.786A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.965A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.288A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.701A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.703A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N SER B 221 " --> pdb=" O PRO B 209 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG B 34 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LEU B 223 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.729A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.873A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN B 122 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.365A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.347A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.541A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.541A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.908A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.019A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.620A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.487A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.158A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.605A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.480A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.815A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.006A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.503A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.657A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.909A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.322A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.688A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2754 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5239 1.33 - 1.45: 4655 1.45 - 1.57: 12799 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22813 Sorted by residual: bond pdb=" CA GLN B 607 " pdb=" CB GLN B 607 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.48e-02 4.57e+03 1.65e+01 bond pdb=" C5 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C5 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.486 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 22808 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 22035 1.83 - 3.66: 7873 3.66 - 5.49: 1090 5.49 - 7.32: 85 7.32 - 9.15: 9 Bond angle restraints: 31092 Sorted by residual: angle pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " pdb=" CG ASN B 122 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA PHE A 106 " pdb=" CB PHE A 106 " pdb=" CG PHE A 106 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA PHE C 559 " pdb=" CB PHE C 559 " pdb=" CG PHE C 559 " ideal model delta sigma weight residual 113.80 119.13 -5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.11 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" CA ASP A 796 " pdb=" CB ASP A 796 " pdb=" CG ASP A 796 " ideal model delta sigma weight residual 112.60 117.88 -5.28 1.00e+00 1.00e+00 2.78e+01 ... (remaining 31087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 13411 17.67 - 35.34: 705 35.34 - 53.00: 112 53.00 - 70.67: 44 70.67 - 88.34: 22 Dihedral angle restraints: 14294 sinusoidal: 5953 harmonic: 8341 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 177.48 -84.48 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 14291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 3820 0.382 - 0.763: 1 0.763 - 1.145: 0 1.145 - 1.526: 0 1.526 - 1.908: 1 Chirality restraints: 3822 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -0.49 -1.91 2.00e-01 2.50e+01 9.10e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.57e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 ... (remaining 3819 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.230 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" CG ASN A 331 " -0.153 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.431 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.329 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.138 2.00e-02 2.50e+03 1.47e-01 2.69e+02 pdb=" CG ASN C1074 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.129 2.00e-02 2.50e+03 1.36e-01 2.32e+02 pdb=" CG ASN A 657 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.209 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.163 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 1 2.16 - 2.85: 6296 2.85 - 3.53: 29937 3.53 - 4.22: 53000 4.22 - 4.90: 91810 Nonbonded interactions: 181044 Sorted by model distance: nonbonded pdb=" OD1 ASN B 343 " pdb=" C1 NAG B1307 " model vdw 1.479 2.776 nonbonded pdb=" OD1 ASN B 343 " pdb=" O5 NAG B1307 " model vdw 2.339 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.493 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.498 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.500 3.040 ... (remaining 181039 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 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 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 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 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 427 or (resid 428 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 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name \ C or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or ( \ resid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 \ through 810 or (resid 811 and (name N or name CA or name C or name O or name CB \ )) or resid 813 through 827 or resid 856 through 866 or (resid 867 through 868 a \ nd (name N or name CA or name C or name O or name CB )) or resid 869 through 920 \ or (resid 921 and (name N or name CA or name C or name O or name CB )) or resid \ 922 through 939 or (resid 940 and (name N or name CA or name C or name O or nam \ e CB )) or resid 941 through 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 name C or name O or name CB )) or resid 990 through 1072 or \ (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 074 through 1117 or (resid 1118 and (name N or name CA or name C or name O or na \ me CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1147 through 1310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name 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 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ 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 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.010 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.440 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.440 22907 Z= 0.906 Angle : 1.825 63.356 31339 Z= 1.183 Chirality : 0.099 1.908 3822 Planarity : 0.012 0.119 3929 Dihedral : 11.913 88.338 8791 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 0.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.11 % Favored : 93.60 % Rotamer: Outliers : 0.27 % Allowed : 1.11 % Favored : 98.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 2797 helix: -0.68 (0.16), residues: 679 sheet: 0.12 (0.23), residues: 449 loop : -0.84 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 273 TYR 0.146 0.020 TYR C 265 PHE 0.110 0.013 PHE A 718 TRP 0.103 0.023 TRP C 886 HIS 0.013 0.003 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.01350 (22813) covalent geometry : angle 1.75754 (31092) SS BOND : bond 0.00966 ( 35) SS BOND : angle 2.27372 ( 70) hydrogen bonds : bond 0.13796 ( 993) hydrogen bonds : angle 8.51532 ( 2754) link_BETA1-4 : bond 0.02481 ( 12) link_BETA1-4 : angle 4.52670 ( 36) link_NAG-ASN : bond 0.21043 ( 47) link_NAG-ASN : angle 7.15259 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 321 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7987 (p0) cc_final: 0.7725 (p0) REVERT: A 564 GLN cc_start: 0.6015 (tp40) cc_final: 0.5813 (tp40) REVERT: C 514 SER cc_start: 0.8732 (t) cc_final: 0.8425 (p) outliers start: 6 outliers final: 1 residues processed: 326 average time/residue: 0.4940 time to fit residues: 190.1812 Evaluate side-chains 155 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN A 314 GLN A 360 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A1010 GLN A1088 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 606 ASN B 907 ASN B 957 GLN B1010 GLN B1088 HIS C 394 ASN C 965 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.149550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108124 restraints weight = 34641.568| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.95 r_work: 0.3487 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22907 Z= 0.151 Angle : 0.704 11.871 31339 Z= 0.354 Chirality : 0.047 0.250 3822 Planarity : 0.004 0.051 3929 Dihedral : 6.088 49.947 4265 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.26 % Allowed : 7.31 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 2797 helix: 0.89 (0.19), residues: 667 sheet: -0.05 (0.19), residues: 629 loop : -0.64 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 983 TYR 0.027 0.002 TYR A 380 PHE 0.025 0.002 PHE B 238 TRP 0.019 0.002 TRP B 64 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00329 (22813) covalent geometry : angle 0.65780 (31092) SS BOND : bond 0.00486 ( 35) SS BOND : angle 1.52257 ( 70) hydrogen bonds : bond 0.04493 ( 993) hydrogen bonds : angle 6.49817 ( 2754) link_BETA1-4 : bond 0.00468 ( 12) link_BETA1-4 : angle 1.78905 ( 36) link_NAG-ASN : bond 0.00431 ( 47) link_NAG-ASN : angle 3.55291 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: A 360 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8120 (t0) REVERT: A 424 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7157 (ptmm) REVERT: A 428 ASP cc_start: 0.8894 (p0) cc_final: 0.8650 (p0) REVERT: A 453 TYR cc_start: 0.7739 (p90) cc_final: 0.7176 (p90) REVERT: A 462 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7696 (mtmm) REVERT: A 641 ASN cc_start: 0.6914 (t0) cc_final: 0.6442 (m110) REVERT: A 988 GLU cc_start: 0.7610 (pm20) cc_final: 0.6971 (pm20) REVERT: A 994 ASP cc_start: 0.8796 (t70) cc_final: 0.8466 (t0) REVERT: A 1038 LYS cc_start: 0.8881 (mttt) cc_final: 0.8679 (mmpt) REVERT: B 985 ASP cc_start: 0.8230 (p0) cc_final: 0.8020 (p0) REVERT: C 517 LEU cc_start: 0.7133 (mm) cc_final: 0.6721 (mt) REVERT: C 735 SER cc_start: 0.8607 (t) cc_final: 0.8233 (p) REVERT: C 983 ARG cc_start: 0.8704 (ttm170) cc_final: 0.8496 (ttp-110) REVERT: C 990 GLU cc_start: 0.7977 (pt0) cc_final: 0.7589 (pp20) outliers start: 51 outliers final: 12 residues processed: 218 average time/residue: 0.5476 time to fit residues: 139.8630 Evaluate side-chains 148 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 44 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN A1048 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN B 907 ASN B 957 GLN B1048 HIS C 394 ASN C 965 GLN C1048 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.149378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107723 restraints weight = 34551.149| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.74 r_work: 0.3514 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22907 Z= 0.128 Angle : 0.609 15.103 31339 Z= 0.309 Chirality : 0.045 0.536 3822 Planarity : 0.004 0.038 3929 Dihedral : 5.468 46.634 4265 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.99 % Allowed : 9.17 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 2797 helix: 1.33 (0.20), residues: 669 sheet: -0.05 (0.19), residues: 620 loop : -0.60 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.022 0.002 TYR C 265 PHE 0.022 0.001 PHE A 168 TRP 0.012 0.001 TRP C 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00282 (22813) covalent geometry : angle 0.57061 (31092) SS BOND : bond 0.00270 ( 35) SS BOND : angle 1.27455 ( 70) hydrogen bonds : bond 0.03984 ( 993) hydrogen bonds : angle 6.02854 ( 2754) link_BETA1-4 : bond 0.00394 ( 12) link_BETA1-4 : angle 1.43712 ( 36) link_NAG-ASN : bond 0.00516 ( 47) link_NAG-ASN : angle 3.06373 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7760 (tm-30) REVERT: A 200 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6871 (m-80) REVERT: A 335 LEU cc_start: 0.9095 (mt) cc_final: 0.8724 (tm) REVERT: A 424 LYS cc_start: 0.7798 (ttmm) cc_final: 0.7237 (ptmm) REVERT: A 428 ASP cc_start: 0.8854 (p0) cc_final: 0.8621 (p0) REVERT: A 453 TYR cc_start: 0.7553 (p90) cc_final: 0.6859 (p90) REVERT: A 462 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7751 (mtmm) REVERT: A 641 ASN cc_start: 0.6899 (t0) cc_final: 0.6584 (m110) REVERT: A 988 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: A 994 ASP cc_start: 0.8847 (t70) cc_final: 0.8499 (t0) REVERT: A 1038 LYS cc_start: 0.8879 (mttt) cc_final: 0.8674 (mmpt) REVERT: B 335 LEU cc_start: 0.8958 (mp) cc_final: 0.8707 (mt) REVERT: B 560 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8121 (mm) REVERT: B 740 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8569 (ttt) REVERT: B 776 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8759 (ttpt) REVERT: B 957 GLN cc_start: 0.8527 (tt0) cc_final: 0.8307 (tt0) REVERT: B 985 ASP cc_start: 0.8111 (p0) cc_final: 0.7900 (p0) REVERT: C 117 LEU cc_start: 0.6863 (mp) cc_final: 0.6479 (tp) REVERT: C 273 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7807 (mmm-85) REVERT: C 517 LEU cc_start: 0.7122 (mm) cc_final: 0.6709 (mt) REVERT: C 574 ASP cc_start: 0.8314 (t70) cc_final: 0.7924 (t0) REVERT: C 990 GLU cc_start: 0.7947 (pt0) cc_final: 0.7734 (pt0) outliers start: 45 outliers final: 14 residues processed: 176 average time/residue: 0.5007 time to fit residues: 105.5290 Evaluate side-chains 144 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 973 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 3 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 15 optimal weight: 0.0070 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN A 564 GLN A 907 ASN A 913 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 907 ASN C 394 ASN C 955 ASN C 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.146103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103838 restraints weight = 34915.493| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.04 r_work: 0.3433 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 22907 Z= 0.217 Angle : 0.633 13.836 31339 Z= 0.319 Chirality : 0.046 0.321 3822 Planarity : 0.004 0.041 3929 Dihedral : 5.219 41.204 4264 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 10.46 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 2797 helix: 1.20 (0.20), residues: 674 sheet: -0.29 (0.19), residues: 682 loop : -0.64 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 273 TYR 0.024 0.002 TYR C1067 PHE 0.023 0.002 PHE C1121 TRP 0.007 0.001 TRP C 886 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00511 (22813) covalent geometry : angle 0.60058 (31092) SS BOND : bond 0.00275 ( 35) SS BOND : angle 1.61323 ( 70) hydrogen bonds : bond 0.04015 ( 993) hydrogen bonds : angle 5.99715 ( 2754) link_BETA1-4 : bond 0.00260 ( 12) link_BETA1-4 : angle 1.31678 ( 36) link_NAG-ASN : bond 0.00391 ( 47) link_NAG-ASN : angle 2.78628 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7817 (tm-30) REVERT: A 335 LEU cc_start: 0.9092 (mt) cc_final: 0.8757 (tm) REVERT: A 424 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7281 (ptmm) REVERT: A 428 ASP cc_start: 0.8855 (p0) cc_final: 0.8616 (p0) REVERT: A 453 TYR cc_start: 0.7521 (p90) cc_final: 0.6838 (p90) REVERT: A 462 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7778 (mtmm) REVERT: A 564 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: A 641 ASN cc_start: 0.6942 (t0) cc_final: 0.6615 (m110) REVERT: A 675 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 988 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: A 994 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8608 (t0) REVERT: B 319 ARG cc_start: 0.8528 (mtm110) cc_final: 0.8067 (mtp180) REVERT: B 335 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8663 (mt) REVERT: B 740 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8668 (ttt) REVERT: B 776 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8829 (ttpt) REVERT: B 957 GLN cc_start: 0.8523 (tt0) cc_final: 0.8286 (tt0) REVERT: B 979 ASP cc_start: 0.7991 (t0) cc_final: 0.7749 (t0) REVERT: C 117 LEU cc_start: 0.6888 (mp) cc_final: 0.6626 (tp) REVERT: C 273 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7761 (mmm-85) REVERT: C 424 LYS cc_start: 0.7883 (tttp) cc_final: 0.7246 (ttmp) REVERT: C 574 ASP cc_start: 0.8259 (t70) cc_final: 0.7835 (t0) REVERT: C 981 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8822 (mm) REVERT: C 986 LYS cc_start: 0.7760 (tppt) cc_final: 0.7480 (tppt) REVERT: C 990 GLU cc_start: 0.7889 (pt0) cc_final: 0.7587 (pt0) outliers start: 54 outliers final: 20 residues processed: 178 average time/residue: 0.4803 time to fit residues: 101.6090 Evaluate side-chains 157 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 40 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 58 optimal weight: 0.5980 chunk 201 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 284 optimal weight: 0.3980 chunk 166 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN C 394 ASN C 965 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.106504 restraints weight = 34403.058| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.82 r_work: 0.3492 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22907 Z= 0.116 Angle : 0.562 13.477 31339 Z= 0.282 Chirality : 0.043 0.240 3822 Planarity : 0.003 0.041 3929 Dihedral : 4.891 39.792 4264 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.73 % Allowed : 12.18 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2797 helix: 1.56 (0.20), residues: 671 sheet: -0.17 (0.19), residues: 641 loop : -0.55 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.021 0.001 TYR A 380 PHE 0.028 0.001 PHE C 168 TRP 0.008 0.001 TRP C 104 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (22813) covalent geometry : angle 0.53037 (31092) SS BOND : bond 0.00229 ( 35) SS BOND : angle 1.57026 ( 70) hydrogen bonds : bond 0.03629 ( 993) hydrogen bonds : angle 5.68291 ( 2754) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.18321 ( 36) link_NAG-ASN : bond 0.00389 ( 47) link_NAG-ASN : angle 2.56316 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7826 (tm-30) REVERT: A 424 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7337 (ptmm) REVERT: A 428 ASP cc_start: 0.8794 (p0) cc_final: 0.8565 (p0) REVERT: A 453 TYR cc_start: 0.7398 (p90) cc_final: 0.6803 (p90) REVERT: A 462 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7786 (mtmm) REVERT: A 641 ASN cc_start: 0.6819 (t0) cc_final: 0.6533 (m110) REVERT: A 675 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 988 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: A 994 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8615 (t0) REVERT: B 335 LEU cc_start: 0.8904 (mp) cc_final: 0.8689 (mt) REVERT: B 560 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 740 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8575 (ttt) REVERT: B 776 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8812 (ttpt) REVERT: B 957 GLN cc_start: 0.8488 (tt0) cc_final: 0.8261 (tt0) REVERT: B 979 ASP cc_start: 0.7945 (t0) cc_final: 0.7703 (t0) REVERT: B 985 ASP cc_start: 0.8049 (p0) cc_final: 0.7842 (p0) REVERT: C 117 LEU cc_start: 0.6799 (mp) cc_final: 0.6559 (tt) REVERT: C 273 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7771 (mmm-85) REVERT: C 424 LYS cc_start: 0.7922 (tttp) cc_final: 0.7319 (ttmp) REVERT: C 574 ASP cc_start: 0.8227 (t70) cc_final: 0.7773 (t0) REVERT: C 900 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: C 981 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8798 (mm) REVERT: C 990 GLU cc_start: 0.7869 (pt0) cc_final: 0.7561 (pt0) outliers start: 39 outliers final: 14 residues processed: 165 average time/residue: 0.4857 time to fit residues: 95.4948 Evaluate side-chains 151 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 89 optimal weight: 0.8980 chunk 128 optimal weight: 50.0000 chunk 270 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 252 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 394 ASN C 914 ASN C 965 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.148688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106624 restraints weight = 34630.096| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.97 r_work: 0.3496 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22907 Z= 0.113 Angle : 0.546 13.193 31339 Z= 0.274 Chirality : 0.043 0.225 3822 Planarity : 0.003 0.043 3929 Dihedral : 4.684 38.704 4264 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 12.58 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2797 helix: 1.71 (0.20), residues: 671 sheet: -0.15 (0.19), residues: 645 loop : -0.49 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.023 0.001 TYR A 380 PHE 0.029 0.001 PHE C 168 TRP 0.007 0.001 TRP A 436 HIS 0.012 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00250 (22813) covalent geometry : angle 0.51729 (31092) SS BOND : bond 0.00188 ( 35) SS BOND : angle 1.32767 ( 70) hydrogen bonds : bond 0.03522 ( 993) hydrogen bonds : angle 5.56064 ( 2754) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.13381 ( 36) link_NAG-ASN : bond 0.00372 ( 47) link_NAG-ASN : angle 2.45178 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7777 (tm-30) REVERT: A 424 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7283 (ptmm) REVERT: A 428 ASP cc_start: 0.8786 (p0) cc_final: 0.8560 (p0) REVERT: A 453 TYR cc_start: 0.7321 (p90) cc_final: 0.6734 (p90) REVERT: A 462 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7713 (mtmm) REVERT: A 641 ASN cc_start: 0.6875 (t0) cc_final: 0.6613 (m110) REVERT: A 675 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: A 988 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: A 994 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (t0) REVERT: B 335 LEU cc_start: 0.8896 (mp) cc_final: 0.8689 (mt) REVERT: B 560 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8023 (mm) REVERT: B 740 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (ttt) REVERT: B 776 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: B 957 GLN cc_start: 0.8495 (tt0) cc_final: 0.8247 (tt0) REVERT: B 994 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (m-30) REVERT: C 117 LEU cc_start: 0.6780 (mp) cc_final: 0.6538 (tt) REVERT: C 273 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7710 (mmm-85) REVERT: C 424 LYS cc_start: 0.7891 (tttp) cc_final: 0.7306 (ttmp) REVERT: C 428 ASP cc_start: 0.8983 (p0) cc_final: 0.8720 (p0) REVERT: C 517 LEU cc_start: 0.7877 (mp) cc_final: 0.7668 (mt) REVERT: C 574 ASP cc_start: 0.8212 (t70) cc_final: 0.7741 (t0) REVERT: C 981 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8795 (mm) REVERT: C 990 GLU cc_start: 0.7819 (pt0) cc_final: 0.7605 (pt0) outliers start: 40 outliers final: 15 residues processed: 173 average time/residue: 0.4700 time to fit residues: 97.5399 Evaluate side-chains 152 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 72 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 540 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN C 394 ASN C 901 GLN C 965 GLN C1101 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.147242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105662 restraints weight = 34606.178| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.16 r_work: 0.3458 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22907 Z= 0.159 Angle : 0.565 13.041 31339 Z= 0.284 Chirality : 0.044 0.240 3822 Planarity : 0.003 0.042 3929 Dihedral : 4.663 36.934 4264 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.17 % Allowed : 12.72 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2797 helix: 1.68 (0.20), residues: 663 sheet: -0.19 (0.19), residues: 647 loop : -0.50 (0.16), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.023 0.001 TYR A 380 PHE 0.025 0.002 PHE B 168 TRP 0.008 0.001 TRP A 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00369 (22813) covalent geometry : angle 0.53667 (31092) SS BOND : bond 0.00213 ( 35) SS BOND : angle 1.60979 ( 70) hydrogen bonds : bond 0.03609 ( 993) hydrogen bonds : angle 5.62850 ( 2754) link_BETA1-4 : bond 0.00296 ( 12) link_BETA1-4 : angle 1.11798 ( 36) link_NAG-ASN : bond 0.00358 ( 47) link_NAG-ASN : angle 2.43244 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7809 (tm-30) REVERT: A 424 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7272 (ptmm) REVERT: A 428 ASP cc_start: 0.8740 (p0) cc_final: 0.8536 (p0) REVERT: A 453 TYR cc_start: 0.7259 (p90) cc_final: 0.6631 (p90) REVERT: A 460 ASN cc_start: 0.8794 (m-40) cc_final: 0.8553 (m-40) REVERT: A 462 LYS cc_start: 0.8097 (mmmm) cc_final: 0.7751 (mtmt) REVERT: A 508 TYR cc_start: 0.7597 (m-80) cc_final: 0.7361 (m-80) REVERT: A 641 ASN cc_start: 0.6959 (t0) cc_final: 0.6696 (m110) REVERT: A 988 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 994 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8683 (t0) REVERT: B 335 LEU cc_start: 0.8877 (mp) cc_final: 0.8660 (mt) REVERT: B 560 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 776 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8875 (ttpt) REVERT: B 957 GLN cc_start: 0.8585 (tt0) cc_final: 0.8327 (tt0) REVERT: C 117 LEU cc_start: 0.6802 (mp) cc_final: 0.6574 (tt) REVERT: C 273 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7740 (mmm-85) REVERT: C 424 LYS cc_start: 0.7915 (tttp) cc_final: 0.7353 (ttmp) REVERT: C 428 ASP cc_start: 0.8981 (p0) cc_final: 0.8718 (p0) REVERT: C 574 ASP cc_start: 0.8219 (t70) cc_final: 0.7757 (t0) REVERT: C 981 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8833 (mm) outliers start: 49 outliers final: 20 residues processed: 167 average time/residue: 0.4321 time to fit residues: 87.3343 Evaluate side-chains 153 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 223 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 188 ASN C 394 ASN C 901 GLN C 965 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.147313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105823 restraints weight = 34484.912| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.23 r_work: 0.3464 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22907 Z= 0.148 Angle : 0.563 12.920 31339 Z= 0.284 Chirality : 0.044 0.304 3822 Planarity : 0.003 0.042 3929 Dihedral : 4.631 36.579 4264 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 13.42 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2797 helix: 1.70 (0.20), residues: 655 sheet: -0.26 (0.19), residues: 662 loop : -0.45 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 983 TYR 0.026 0.001 TYR A 380 PHE 0.027 0.001 PHE C 168 TRP 0.009 0.001 TRP A 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00342 (22813) covalent geometry : angle 0.53099 (31092) SS BOND : bond 0.00195 ( 35) SS BOND : angle 2.11414 ( 70) hydrogen bonds : bond 0.03560 ( 993) hydrogen bonds : angle 5.59757 ( 2754) link_BETA1-4 : bond 0.00294 ( 12) link_BETA1-4 : angle 1.09023 ( 36) link_NAG-ASN : bond 0.00359 ( 47) link_NAG-ASN : angle 2.39716 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7784 (tm-30) REVERT: A 424 LYS cc_start: 0.7820 (ttmm) cc_final: 0.7280 (ptmm) REVERT: A 453 TYR cc_start: 0.7221 (p90) cc_final: 0.6660 (p90) REVERT: A 460 ASN cc_start: 0.8724 (m-40) cc_final: 0.8456 (m-40) REVERT: A 462 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7774 (mtmt) REVERT: A 641 ASN cc_start: 0.6904 (t0) cc_final: 0.6691 (m110) REVERT: A 675 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 988 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: B 335 LEU cc_start: 0.8875 (mp) cc_final: 0.8658 (mt) REVERT: B 560 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (mm) REVERT: B 776 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8853 (ttpt) REVERT: B 817 PHE cc_start: 0.8513 (t80) cc_final: 0.8063 (t80) REVERT: B 994 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: C 273 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7702 (mmm-85) REVERT: C 424 LYS cc_start: 0.7828 (tttp) cc_final: 0.7261 (ttmp) REVERT: C 574 ASP cc_start: 0.8200 (t70) cc_final: 0.7732 (t0) REVERT: C 950 ASP cc_start: 0.8386 (p0) cc_final: 0.8136 (p0) REVERT: C 981 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8806 (mm) outliers start: 42 outliers final: 18 residues processed: 162 average time/residue: 0.4466 time to fit residues: 87.1795 Evaluate side-chains 151 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 260 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN B 317 ASN B 907 ASN B 957 GLN C 394 ASN C 901 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104836 restraints weight = 34725.325| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.96 r_work: 0.3442 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22907 Z= 0.180 Angle : 0.580 12.870 31339 Z= 0.292 Chirality : 0.045 0.336 3822 Planarity : 0.004 0.042 3929 Dihedral : 4.651 35.961 4264 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.77 % Allowed : 13.65 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2797 helix: 1.59 (0.20), residues: 664 sheet: -0.32 (0.19), residues: 661 loop : -0.44 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.026 0.002 TYR A 380 PHE 0.025 0.002 PHE B 168 TRP 0.017 0.001 TRP A 436 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00423 (22813) covalent geometry : angle 0.54997 (31092) SS BOND : bond 0.00198 ( 35) SS BOND : angle 2.01527 ( 70) hydrogen bonds : bond 0.03618 ( 993) hydrogen bonds : angle 5.65110 ( 2754) link_BETA1-4 : bond 0.00271 ( 12) link_BETA1-4 : angle 1.09444 ( 36) link_NAG-ASN : bond 0.00358 ( 47) link_NAG-ASN : angle 2.40296 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7832 (tm-30) REVERT: A 424 LYS cc_start: 0.7855 (ttmm) cc_final: 0.7295 (ptmm) REVERT: A 453 TYR cc_start: 0.7246 (p90) cc_final: 0.6709 (p90) REVERT: A 460 ASN cc_start: 0.8703 (m-40) cc_final: 0.8435 (m-40) REVERT: A 462 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7778 (mtmt) REVERT: A 508 TYR cc_start: 0.7574 (m-80) cc_final: 0.7234 (m-80) REVERT: A 641 ASN cc_start: 0.6942 (t0) cc_final: 0.6736 (m110) REVERT: A 675 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: A 988 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: A 1072 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: B 190 ARG cc_start: 0.7409 (mtt90) cc_final: 0.6590 (mmt90) REVERT: B 335 LEU cc_start: 0.8888 (mp) cc_final: 0.8668 (mt) REVERT: B 560 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 776 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8914 (ttpt) REVERT: C 273 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7817 (mmm-85) REVERT: C 424 LYS cc_start: 0.7951 (tttp) cc_final: 0.7410 (ttmp) REVERT: C 574 ASP cc_start: 0.8228 (t70) cc_final: 0.7770 (t0) REVERT: C 950 ASP cc_start: 0.8478 (p0) cc_final: 0.8269 (p0) REVERT: C 981 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8821 (mm) outliers start: 40 outliers final: 22 residues processed: 163 average time/residue: 0.4656 time to fit residues: 90.7595 Evaluate side-chains 157 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 30.0000 chunk 227 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 394 ASN C 901 GLN C1101 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104041 restraints weight = 34819.325| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.93 r_work: 0.3420 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 22907 Z= 0.231 Angle : 0.617 12.859 31339 Z= 0.311 Chirality : 0.046 0.325 3822 Planarity : 0.004 0.040 3929 Dihedral : 4.857 36.743 4264 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.68 % Allowed : 14.05 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2797 helix: 1.32 (0.20), residues: 673 sheet: -0.45 (0.19), residues: 661 loop : -0.50 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 983 TYR 0.029 0.002 TYR A 380 PHE 0.029 0.002 PHE C1121 TRP 0.008 0.001 TRP B 886 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00543 (22813) covalent geometry : angle 0.58750 (31092) SS BOND : bond 0.00237 ( 35) SS BOND : angle 2.08324 ( 70) hydrogen bonds : bond 0.03808 ( 993) hydrogen bonds : angle 5.82351 ( 2754) link_BETA1-4 : bond 0.00223 ( 12) link_BETA1-4 : angle 1.11236 ( 36) link_NAG-ASN : bond 0.00376 ( 47) link_NAG-ASN : angle 2.47595 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7831 (tm-30) REVERT: A 231 ILE cc_start: 0.7218 (pt) cc_final: 0.6904 (tt) REVERT: A 424 LYS cc_start: 0.7851 (ttmm) cc_final: 0.7208 (ptmm) REVERT: A 453 TYR cc_start: 0.7224 (p90) cc_final: 0.6691 (p90) REVERT: A 460 ASN cc_start: 0.8785 (m-40) cc_final: 0.8551 (m-40) REVERT: A 462 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7838 (mtmt) REVERT: A 1072 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: B 190 ARG cc_start: 0.7450 (mtt90) cc_final: 0.6717 (mmt90) REVERT: B 335 LEU cc_start: 0.8903 (mp) cc_final: 0.8699 (mt) REVERT: B 776 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8926 (ttpt) REVERT: B 994 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8492 (m-30) REVERT: C 273 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7843 (mmm-85) REVERT: C 424 LYS cc_start: 0.8010 (tttp) cc_final: 0.7457 (ttmp) REVERT: C 574 ASP cc_start: 0.8244 (t70) cc_final: 0.7748 (t0) REVERT: C 950 ASP cc_start: 0.8562 (p0) cc_final: 0.8301 (p0) REVERT: C 981 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8802 (mm) outliers start: 38 outliers final: 23 residues processed: 151 average time/residue: 0.5078 time to fit residues: 90.4562 Evaluate side-chains 141 residues out of total 2520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 394 ASN C1101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.147713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105833 restraints weight = 34491.819| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.08 r_work: 0.3466 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22907 Z= 0.127 Angle : 0.553 12.651 31339 Z= 0.277 Chirality : 0.044 0.260 3822 Planarity : 0.003 0.041 3929 Dihedral : 4.603 35.397 4264 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.42 % Allowed : 14.71 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.16), residues: 2797 helix: 1.68 (0.20), residues: 663 sheet: -0.32 (0.19), residues: 631 loop : -0.38 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 983 TYR 0.028 0.001 TYR A 380 PHE 0.028 0.001 PHE C 168 TRP 0.009 0.001 TRP C 104 HIS 0.011 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00289 (22813) covalent geometry : angle 0.52599 (31092) SS BOND : bond 0.00188 ( 35) SS BOND : angle 1.68552 ( 70) hydrogen bonds : bond 0.03441 ( 993) hydrogen bonds : angle 5.55444 ( 2754) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.00420 ( 36) link_NAG-ASN : bond 0.00371 ( 47) link_NAG-ASN : angle 2.29458 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7442.85 seconds wall clock time: 127 minutes 28.88 seconds (7648.88 seconds total)