Starting phenix.real_space_refine on Mon Jul 6 02:41:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yqy_34039/07_2026/7yqy_34039.cif" } resolution = 3.74 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= 0.053 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 132 5.16 5 C 20289 2.51 5 N 5271 2.21 5 O 6291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31983 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 8544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8544 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 58, 'TRANS': 1038} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} 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 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 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 chiralities: 2 Chain: "M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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 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 chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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 chiralities: 13 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.30, per 1000 atoms: 0.23 Number of scatterers: 31983 At special positions: 0 Unit cell: (188.32, 160.5, 185.11, 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 132 16.00 O 6291 8.00 N 5271 7.00 C 20289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 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=11, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " BETA1-6 " NAG M 1 " - " FUC M 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 4 " " NAG U 1 " - " FUC U 4 " NAG-ASN " NAG A1305 " - " ASN A 282 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 657 " " NAG A1310 " - " ASN A 709 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A1134 " " NAG A1313 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 74 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 149 " " NAG B1305 " - " ASN B 165 " " NAG B1306 " - " ASN B 234 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 331 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 74 " " NAG C1305 " - " ASN C 122 " " NAG C1306 " - " ASN C 149 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 282 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG C1316 " - " ASN C 331 " " NAG D 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1074 " Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7386 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 56 sheets defined 17.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 removed outlier: 4.187A pdb=" N GLY A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.572A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.907A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.551A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.531A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (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 760 through 782 removed outlier: 3.565A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.657A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 869 through 880 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.820A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.860A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.092A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.795A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.841A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.094A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.563A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.839A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.069A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.748A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.703A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.529A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.933A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 880 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.507A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.883A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.882A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.953A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1030 removed outlier: 3.584A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B1006 " --> pdb=" O GLN B1002 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.103A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.765A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.595A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.598A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 782 removed outlier: 3.997A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.504A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 3.598A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 869 through 881 removed outlier: 3.562A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.590A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.985A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.796A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.872A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.660A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.974A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.926A 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 removed outlier: 4.025A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 7.544A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.181A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.422A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.709A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (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 660 removed outlier: 3.983A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.521A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.574A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.574A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.429A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.941A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.293A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.933A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 356 through 357 removed outlier: 3.618A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.836A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.930A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.509A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.131A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 725 through 727 removed outlier: 3.622A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD1, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD4, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.154A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.705A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 108 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN C 115 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 205 through 208 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.852A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.594A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 355 through 357 removed outlier: 3.571A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.072A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.736A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 718 through 722 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 722 removed outlier: 7.304A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AE7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AE8, first strand: chain 'F' and resid 19 through 22 Processing sheet with id=AE9, first strand: chain 'F' and resid 45 through 49 removed outlier: 6.636A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.764A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 46 through 49 removed outlier: 6.562A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 45 through 51 removed outlier: 5.684A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 49 through 51 removed outlier: 3.980A pdb=" N GLY I 33 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'J' and resid 49 through 51 removed outlier: 4.505A pdb=" N ASN J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 49 through 51 Processing sheet with id=AG1, first strand: chain 'E' and resid 19 through 22 removed outlier: 3.858A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 46 through 49 removed outlier: 3.824A pdb=" N ARG E 46 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN E 91 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR E 97 " --> pdb=" O GLN E 91 " (cutoff:3.500A) 835 hydrogen bonds defined for protein. 2208 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: 7.34 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5453 1.32 - 1.45: 9263 1.45 - 1.58: 17834 1.58 - 1.70: 3 1.70 - 1.83: 168 Bond restraints: 32721 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" CG LEU B 441 " pdb=" CD1 LEU B 441 " ideal model delta sigma weight residual 1.521 1.620 -0.099 3.30e-02 9.18e+02 8.99e+00 bond pdb=" N ILE B 332 " pdb=" CA ILE B 332 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.17e-02 7.31e+03 8.27e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.18e+00 ... (remaining 32716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 44270 3.09 - 6.19: 245 6.19 - 9.28: 18 9.28 - 12.38: 0 12.38 - 15.47: 2 Bond angle restraints: 44535 Sorted by residual: angle pdb=" C LEU A 984 " pdb=" N ASP A 985 " pdb=" CA ASP A 985 " ideal model delta sigma weight residual 121.61 129.21 -7.60 1.39e+00 5.18e-01 2.99e+01 angle pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " pdb=" CD1 LEU B 441 " ideal model delta sigma weight residual 110.70 126.17 -15.47 3.00e+00 1.11e-01 2.66e+01 angle pdb=" N THR A 333 " pdb=" CA THR A 333 " pdb=" C THR A 333 " ideal model delta sigma weight residual 114.62 108.95 5.67 1.14e+00 7.69e-01 2.47e+01 angle pdb=" CB LEU B 441 " pdb=" CG LEU B 441 " pdb=" CD2 LEU B 441 " ideal model delta sigma weight residual 110.70 123.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA PHE C 329 " pdb=" CB PHE C 329 " pdb=" CG PHE C 329 " ideal model delta sigma weight residual 113.80 117.91 -4.11 1.00e+00 1.00e+00 1.69e+01 ... (remaining 44530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 16942 17.61 - 35.22: 1512 35.22 - 52.84: 273 52.84 - 70.45: 41 70.45 - 88.06: 45 Dihedral angle restraints: 18813 sinusoidal: 7275 harmonic: 11538 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 2.06 -88.06 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -4.02 -81.98 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.69 -62.31 1 1.00e+01 1.00e-02 5.14e+01 ... (remaining 18810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.546: 5206 0.546 - 1.092: 1 1.092 - 1.638: 0 1.638 - 2.184: 0 2.184 - 2.730: 1 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CG LEU B 441 " pdb=" CB LEU B 441 " pdb=" CD1 LEU B 441 " pdb=" CD2 LEU B 441 " both_signs ideal model delta sigma weight residual False -2.59 0.14 -2.73 2.00e-01 2.50e+01 1.86e+02 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 5205 not shown) Planarity restraints: 5715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1316 " 0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C1316 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1316 " 0.122 2.00e-02 2.50e+03 pdb=" N2 NAG C1316 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG C1316 " 0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1313 " -0.316 2.00e-02 2.50e+03 2.70e-01 9.14e+02 pdb=" C7 NAG A1313 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG A1313 " -0.002 2.00e-02 2.50e+03 pdb=" N2 NAG A1313 " 0.463 2.00e-02 2.50e+03 pdb=" O7 NAG A1313 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.033 2.00e-02 2.50e+03 6.76e-02 5.72e+01 pdb=" C7 NAG B1309 " -0.128 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.007 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.044 2.00e-02 2.50e+03 ... (remaining 5712 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 252 2.52 - 3.12: 24153 3.12 - 3.71: 46927 3.71 - 4.31: 63868 4.31 - 4.90: 105529 Nonbonded interactions: 240729 Sorted by model distance: nonbonded pdb=" CD2 LEU B 441 " pdb=" O7 NAG B1309 " model vdw 1.925 2.768 nonbonded pdb=" CD1 LEU B 441 " pdb=" O7 NAG B1309 " model vdw 2.051 2.768 nonbonded pdb=" CE1 PHE C 374 " pdb=" O3 NAG U 1 " model vdw 2.135 2.672 nonbonded pdb=" O ALA I 24 " pdb=" OG1 THR I 77 " model vdw 2.160 3.040 nonbonded pdb=" OG SER J 35 " pdb=" OD2 ASP J 99 " model vdw 2.160 3.040 ... (remaining 240724 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' selection = (chain 'B' and resid 25 through 1313) selection = (chain 'C' and resid 25 through 1313) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = (chain 'J' and resid 1 through 123) } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } 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 group one per residue 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.170 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.004 0.099 32834 Z= 0.180 Angle : 0.682 15.474 44802 Z= 0.334 Chirality : 0.062 2.730 5208 Planarity : 0.007 0.295 5670 Dihedral : 14.014 87.522 11310 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.98 % Favored : 90.95 % Rotamer: Outliers : 0.18 % Allowed : 0.32 % Favored : 99.50 % 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: -2.25 (0.13), residues: 3954 helix: -1.15 (0.21), residues: 590 sheet: -0.53 (0.19), residues: 754 loop : -1.98 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.022 0.001 TYR I 100 PHE 0.036 0.001 PHE C 374 TRP 0.035 0.002 TRP H 47 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (32721) covalent geometry : angle 0.65396 / 0.33 (44535) SS BOND : bond 0.00230 / 0.14 ( 39) SS BOND : angle 1.08070 / 0.75 ( 78) hydrogen bonds : bond 0.26799 / 18.16 ( 812) hydrogen bonds : angle 8.99506 / 6.15 ( 2208) Misc. bond : bond 0.01509 / 1.10 ( 11) link_BETA1-4 : bond 0.00576 / 0.32 ( 15) link_BETA1-4 : angle 2.36043 / 1.35 ( 45) link_BETA1-6 : bond 0.00436 / 0.21 ( 3) link_BETA1-6 : angle 1.57349 / 0.88 ( 9) link_NAG-ASN : bond 0.00591 / 0.37 ( 45) link_NAG-ASN : angle 3.26159 / 2.04 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 243 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7610 (m-80) cc_final: 0.7181 (m-10) REVERT: F 59 ILE cc_start: 0.7027 (mp) cc_final: 0.5902 (mp) REVERT: F 72 PHE cc_start: 0.6192 (m-80) cc_final: 0.5865 (m-80) REVERT: G 46 ARG cc_start: 0.7344 (mpp-170) cc_final: 0.5876 (mmp-170) REVERT: H 80 TYR cc_start: 0.8176 (m-10) cc_final: 0.7918 (m-10) REVERT: I 48 MET cc_start: 0.3151 (ppp) cc_final: 0.2625 (ppp) REVERT: I 70 MET cc_start: 0.2173 (ptt) cc_final: 0.0298 (ptt) REVERT: I 80 TYR cc_start: 0.6414 (m-80) cc_final: 0.5213 (m-80) REVERT: J 57 ASN cc_start: 0.7545 (p0) cc_final: 0.7138 (p0) REVERT: J 70 MET cc_start: 0.5250 (mmp) cc_final: 0.4734 (mpp) outliers start: 6 outliers final: 4 residues processed: 249 average time/residue: 0.1966 time to fit residues: 81.3975 Evaluate side-chains 179 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C1106 GLN F 38 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 119 GLN J 59 ASN E 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.138126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092532 restraints weight = 87476.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090111 restraints weight = 57698.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090207 restraints weight = 58540.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090590 restraints weight = 51005.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.090718 restraints weight = 48297.940| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32834 Z= 0.212 Angle : 0.712 12.510 44802 Z= 0.351 Chirality : 0.049 0.484 5208 Planarity : 0.005 0.073 5670 Dihedral : 4.903 41.686 4306 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 0.76 % Allowed : 8.17 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.25 (0.13), residues: 3954 helix: -0.50 (0.21), residues: 632 sheet: -0.76 (0.18), residues: 806 loop : -2.13 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.025 0.002 TYR A1067 PHE 0.045 0.002 PHE C 374 TRP 0.039 0.002 TRP H 47 HIS 0.006 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (32721) covalent geometry : angle 0.68703 / 0.35 (44535) SS BOND : bond 0.00322 / 0.20 ( 39) SS BOND : angle 1.53077 / 1.05 ( 78) hydrogen bonds : bond 0.06434 / 4.22 ( 812) hydrogen bonds : angle 6.39834 / 4.37 ( 2208) Misc. bond : bond 0.00911 / 0.47 ( 11) link_BETA1-4 : bond 0.00697 / 0.42 ( 15) link_BETA1-4 : angle 2.11680 / 1.23 ( 45) link_BETA1-6 : bond 0.00430 / 0.17 ( 3) link_BETA1-6 : angle 1.41807 / 0.78 ( 9) link_NAG-ASN : bond 0.00611 / 0.39 ( 45) link_NAG-ASN : angle 3.06598 / 1.96 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.254 Fit side-chains REVERT: A 65 PHE cc_start: 0.7661 (m-80) cc_final: 0.7173 (m-10) REVERT: A 100 ILE cc_start: 0.8600 (mm) cc_final: 0.8343 (mp) REVERT: A 353 TRP cc_start: 0.5038 (OUTLIER) cc_final: 0.2876 (m-90) REVERT: B 52 GLN cc_start: 0.8345 (tp40) cc_final: 0.8111 (tp40) REVERT: B 1017 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 1030 SER cc_start: 0.9305 (m) cc_final: 0.8902 (t) REVERT: C 177 MET cc_start: 0.5964 (tpp) cc_final: 0.5668 (tpp) REVERT: C 403 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7311 (tpp80) REVERT: C 957 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 46 ARG cc_start: 0.7220 (mpp-170) cc_final: 0.5965 (mmp-170) REVERT: H 29 PHE cc_start: 0.8695 (t80) cc_final: 0.8455 (t80) REVERT: I 48 MET cc_start: 0.3004 (ppp) cc_final: 0.2586 (ppp) REVERT: I 70 MET cc_start: 0.1797 (ptt) cc_final: 0.1532 (ptt) REVERT: I 80 TYR cc_start: 0.6637 (m-80) cc_final: 0.5565 (m-80) REVERT: J 57 ASN cc_start: 0.7610 (p0) cc_final: 0.7032 (p0) REVERT: J 70 MET cc_start: 0.5267 (mmt) cc_final: 0.4730 (mpp) outliers start: 26 outliers final: 16 residues processed: 209 average time/residue: 0.2087 time to fit residues: 71.3924 Evaluate side-chains 182 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 255 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 346 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 0.3980 chunk 227 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 580 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093005 restraints weight = 87271.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.092452 restraints weight = 61568.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092019 restraints weight = 50903.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092256 restraints weight = 52686.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092452 restraints weight = 46678.914| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32834 Z= 0.120 Angle : 0.637 12.954 44802 Z= 0.309 Chirality : 0.047 0.438 5208 Planarity : 0.004 0.066 5670 Dihedral : 4.586 38.971 4301 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.67 % Favored : 91.30 % Rotamer: Outliers : 1.32 % Allowed : 10.33 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.13), residues: 3954 helix: -0.10 (0.21), residues: 633 sheet: -0.66 (0.18), residues: 814 loop : -2.08 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 102 TYR 0.032 0.001 TYR F 50 PHE 0.034 0.001 PHE C 374 TRP 0.042 0.002 TRP H 47 HIS 0.008 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (32721) covalent geometry : angle 0.61303 / 0.30 (44535) SS BOND : bond 0.00228 / 0.15 ( 39) SS BOND : angle 1.16786 / 0.81 ( 78) hydrogen bonds : bond 0.05434 / 3.57 ( 812) hydrogen bonds : angle 5.82247 / 3.98 ( 2208) Misc. bond : bond 0.00529 / 0.34 ( 11) link_BETA1-4 : bond 0.00587 / 0.35 ( 15) link_BETA1-4 : angle 1.95135 / 1.12 ( 45) link_BETA1-6 : bond 0.00757 / 0.36 ( 3) link_BETA1-6 : angle 1.17090 / 0.62 ( 9) link_NAG-ASN : bond 0.00634 / 0.40 ( 45) link_NAG-ASN : angle 2.92897 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7648 (m-80) cc_final: 0.7276 (m-10) REVERT: A 353 TRP cc_start: 0.4885 (OUTLIER) cc_final: 0.2871 (m-90) REVERT: B 52 GLN cc_start: 0.8124 (tp40) cc_final: 0.7885 (tp40) REVERT: B 332 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 1030 SER cc_start: 0.9222 (m) cc_final: 0.8955 (t) REVERT: C 237 ARG cc_start: 0.6699 (ptt-90) cc_final: 0.6295 (ptt-90) REVERT: C 403 ARG cc_start: 0.7839 (tpt170) cc_final: 0.7558 (tpp80) REVERT: C 957 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8399 (tm-30) REVERT: F 72 PHE cc_start: 0.6714 (m-80) cc_final: 0.6367 (m-80) REVERT: G 46 ARG cc_start: 0.7170 (mpp-170) cc_final: 0.5991 (mmp-170) REVERT: H 45 LEU cc_start: 0.8280 (mp) cc_final: 0.7534 (tp) REVERT: H 102 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.6950 (tpp-160) REVERT: I 80 TYR cc_start: 0.6508 (m-80) cc_final: 0.5421 (m-80) REVERT: J 57 ASN cc_start: 0.7612 (p0) cc_final: 0.6979 (p0) REVERT: J 70 MET cc_start: 0.5172 (mmt) cc_final: 0.4642 (mpp) outliers start: 45 outliers final: 23 residues processed: 238 average time/residue: 0.1858 time to fit residues: 73.6168 Evaluate side-chains 197 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 206 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 544 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1036 GLN C 196 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN H 43 GLN H 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.137942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092170 restraints weight = 86816.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.089500 restraints weight = 58877.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.089816 restraints weight = 58935.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090103 restraints weight = 54197.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090211 restraints weight = 48770.120| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32834 Z= 0.191 Angle : 0.675 11.628 44802 Z= 0.328 Chirality : 0.048 0.470 5208 Planarity : 0.004 0.087 5670 Dihedral : 4.726 39.766 4301 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.71 % Favored : 90.26 % Rotamer: Outliers : 1.96 % Allowed : 12.70 % Favored : 85.34 % 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: -2.12 (0.13), residues: 3954 helix: -0.15 (0.21), residues: 639 sheet: -0.64 (0.19), residues: 784 loop : -2.12 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 509 TYR 0.024 0.002 TYR F 50 PHE 0.031 0.002 PHE C 374 TRP 0.052 0.002 TRP H 47 HIS 0.007 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (32721) covalent geometry : angle 0.65243 / 0.32 (44535) SS BOND : bond 0.00295 / 0.19 ( 39) SS BOND : angle 1.24989 / 0.85 ( 78) hydrogen bonds : bond 0.05447 / 3.59 ( 812) hydrogen bonds : angle 5.82063 / 3.96 ( 2208) Misc. bond : bond 0.00503 / 0.32 ( 11) link_BETA1-4 : bond 0.00630 / 0.38 ( 15) link_BETA1-4 : angle 1.85310 / 1.06 ( 45) link_BETA1-6 : bond 0.00609 / 0.28 ( 3) link_BETA1-6 : angle 1.31921 / 0.72 ( 9) link_NAG-ASN : bond 0.00573 / 0.37 ( 45) link_NAG-ASN : angle 2.90231 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7576 (m-80) cc_final: 0.7193 (m-10) REVERT: A 100 ILE cc_start: 0.8598 (mm) cc_final: 0.8333 (mp) REVERT: A 353 TRP cc_start: 0.5247 (OUTLIER) cc_final: 0.3036 (m-90) REVERT: A 630 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.4021 (t) REVERT: A 820 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (t0) REVERT: A 855 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.6387 (m-10) REVERT: B 1029 MET cc_start: 0.8513 (ttm) cc_final: 0.8277 (ttt) REVERT: B 1030 SER cc_start: 0.9262 (m) cc_final: 0.9030 (t) REVERT: C 190 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7356 (ttt90) REVERT: C 957 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8366 (tm-30) REVERT: G 46 ARG cc_start: 0.7236 (mpp-170) cc_final: 0.6302 (mmp-170) REVERT: H 29 PHE cc_start: 0.8665 (t80) cc_final: 0.8366 (t80) REVERT: H 45 LEU cc_start: 0.8390 (mp) cc_final: 0.7635 (tp) REVERT: H 122 LEU cc_start: 0.6833 (tt) cc_final: 0.6359 (mt) REVERT: I 48 MET cc_start: 0.2736 (ppp) cc_final: 0.2205 (pmm) REVERT: I 70 MET cc_start: 0.2034 (ptt) cc_final: 0.1251 (ptt) REVERT: I 80 TYR cc_start: 0.6552 (m-80) cc_final: 0.5485 (m-80) REVERT: J 57 ASN cc_start: 0.7487 (p0) cc_final: 0.6835 (p0) REVERT: J 70 MET cc_start: 0.5199 (mmt) cc_final: 0.4820 (mpp) outliers start: 67 outliers final: 33 residues processed: 232 average time/residue: 0.1878 time to fit residues: 72.3079 Evaluate side-chains 201 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 276 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 350 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 190 optimal weight: 0.2980 chunk 246 optimal weight: 0.0170 chunk 339 optimal weight: 0.8980 chunk 367 optimal weight: 7.9990 chunk 368 optimal weight: 50.0000 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 580 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.139152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093135 restraints weight = 86951.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.091583 restraints weight = 60691.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091586 restraints weight = 57698.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.091986 restraints weight = 52110.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092076 restraints weight = 47647.646| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32834 Z= 0.116 Angle : 0.628 11.719 44802 Z= 0.304 Chirality : 0.046 0.432 5208 Planarity : 0.004 0.073 5670 Dihedral : 4.514 37.908 4301 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.70 % Favored : 91.25 % Rotamer: Outliers : 1.81 % Allowed : 13.84 % Favored : 84.34 % 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: -2.00 (0.13), residues: 3954 helix: 0.15 (0.21), residues: 629 sheet: -0.56 (0.18), residues: 818 loop : -2.11 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 102 TYR 0.019 0.001 TYR F 50 PHE 0.039 0.001 PHE C 374 TRP 0.055 0.002 TRP H 47 HIS 0.006 0.000 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (32721) covalent geometry : angle 0.60611 / 0.30 (44535) SS BOND : bond 0.00324 / 0.21 ( 39) SS BOND : angle 1.10405 / 0.75 ( 78) hydrogen bonds : bond 0.04714 / 3.09 ( 812) hydrogen bonds : angle 5.48526 / 3.74 ( 2208) Misc. bond : bond 0.00541 / 0.33 ( 11) link_BETA1-4 : bond 0.00541 / 0.32 ( 15) link_BETA1-4 : angle 1.78458 / 1.02 ( 45) link_BETA1-6 : bond 0.00746 / 0.34 ( 3) link_BETA1-6 : angle 1.13680 / 0.61 ( 9) link_NAG-ASN : bond 0.00559 / 0.37 ( 45) link_NAG-ASN : angle 2.83156 / 1.80 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7499 (m-80) cc_final: 0.7137 (m-10) REVERT: A 630 THR cc_start: 0.3940 (OUTLIER) cc_final: 0.3712 (t) REVERT: A 855 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: C 237 ARG cc_start: 0.6961 (ptt-90) cc_final: 0.6496 (ptt-90) REVERT: C 403 ARG cc_start: 0.7843 (tpt-90) cc_final: 0.7579 (tpp-160) REVERT: C 957 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8295 (tm-30) REVERT: G 46 ARG cc_start: 0.7132 (mpp-170) cc_final: 0.6223 (mmp-170) REVERT: H 29 PHE cc_start: 0.8619 (t80) cc_final: 0.8414 (t80) REVERT: H 45 LEU cc_start: 0.8313 (mp) cc_final: 0.7570 (tp) REVERT: H 102 ARG cc_start: 0.7438 (tpp-160) cc_final: 0.7021 (tpp-160) REVERT: H 122 LEU cc_start: 0.6763 (tt) cc_final: 0.6277 (mt) REVERT: I 80 TYR cc_start: 0.6612 (m-80) cc_final: 0.5558 (m-80) REVERT: J 57 ASN cc_start: 0.7488 (p0) cc_final: 0.6824 (p0) REVERT: J 70 MET cc_start: 0.5220 (mmt) cc_final: 0.4872 (mpp) outliers start: 62 outliers final: 34 residues processed: 240 average time/residue: 0.1908 time to fit residues: 75.8270 Evaluate side-chains 207 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain I residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 99 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 116 optimal weight: 0.0040 chunk 19 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 196 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 119 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.091269 restraints weight = 86989.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089200 restraints weight = 57487.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.089512 restraints weight = 54785.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089755 restraints weight = 50518.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089968 restraints weight = 45988.559| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32834 Z= 0.180 Angle : 0.669 11.731 44802 Z= 0.324 Chirality : 0.048 0.455 5208 Planarity : 0.004 0.063 5670 Dihedral : 4.680 37.591 4301 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.91 % Favored : 90.06 % Rotamer: Outliers : 2.43 % Allowed : 14.22 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3954 helix: 0.06 (0.21), residues: 635 sheet: -0.59 (0.19), residues: 786 loop : -2.13 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 102 TYR 0.020 0.001 TYR A1067 PHE 0.032 0.002 PHE C 374 TRP 0.061 0.002 TRP H 47 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (32721) covalent geometry : angle 0.64428 / 0.32 (44535) SS BOND : bond 0.00496 / 0.26 ( 39) SS BOND : angle 1.72086 / 1.33 ( 78) hydrogen bonds : bond 0.05065 / 3.33 ( 812) hydrogen bonds : angle 5.58526 / 3.80 ( 2208) Misc. bond : bond 0.00539 / 0.34 ( 11) link_BETA1-4 : bond 0.00612 / 0.37 ( 15) link_BETA1-4 : angle 1.77573 / 1.01 ( 45) link_BETA1-6 : bond 0.00522 / 0.24 ( 3) link_BETA1-6 : angle 1.32303 / 0.74 ( 9) link_NAG-ASN : bond 0.00538 / 0.35 ( 45) link_NAG-ASN : angle 2.91910 / 1.85 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 1.219 Fit side-chains REVERT: A 65 PHE cc_start: 0.7740 (m-80) cc_final: 0.7375 (m-10) REVERT: A 100 ILE cc_start: 0.8612 (mm) cc_final: 0.8347 (mp) REVERT: A 630 THR cc_start: 0.4303 (OUTLIER) cc_final: 0.4041 (t) REVERT: A 855 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.6499 (m-10) REVERT: B 759 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7438 (t80) REVERT: B 906 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.7934 (t80) REVERT: C 190 ARG cc_start: 0.7728 (mtt90) cc_final: 0.7107 (ttt90) REVERT: C 403 ARG cc_start: 0.7779 (tpt-90) cc_final: 0.7468 (tpp-160) REVERT: C 697 MET cc_start: 0.7423 (mtt) cc_final: 0.7146 (mtt) REVERT: C 957 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8319 (tm-30) REVERT: G 46 ARG cc_start: 0.7129 (mpp-170) cc_final: 0.6334 (mmp-170) REVERT: H 29 PHE cc_start: 0.8719 (t80) cc_final: 0.8514 (t80) REVERT: H 45 LEU cc_start: 0.8319 (mp) cc_final: 0.7557 (tp) REVERT: I 48 MET cc_start: 0.2881 (ppp) cc_final: 0.2205 (pmm) REVERT: I 80 TYR cc_start: 0.6582 (m-80) cc_final: 0.5479 (m-80) REVERT: J 57 ASN cc_start: 0.7450 (p0) cc_final: 0.6741 (p0) REVERT: J 70 MET cc_start: 0.5231 (mmt) cc_final: 0.4882 (mpp) outliers start: 83 outliers final: 48 residues processed: 246 average time/residue: 0.1789 time to fit residues: 73.7172 Evaluate side-chains 214 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 68 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 348 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 chunk 373 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 368 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 237 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 196 ASN C 343 ASN C 437 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 65 GLN H 119 GLN I 116 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088018 restraints weight = 87650.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086590 restraints weight = 57294.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.086806 restraints weight = 51274.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.087063 restraints weight = 51830.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087303 restraints weight = 44630.785| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 32834 Z= 0.308 Angle : 0.800 12.137 44802 Z= 0.391 Chirality : 0.052 0.506 5208 Planarity : 0.005 0.062 5670 Dihedral : 5.276 36.949 4301 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.63 % Favored : 88.34 % Rotamer: Outliers : 2.63 % Allowed : 15.42 % Favored : 81.94 % 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: -2.38 (0.13), residues: 3954 helix: -0.33 (0.21), residues: 628 sheet: -0.96 (0.18), residues: 799 loop : -2.25 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 466 TYR 0.026 0.002 TYR A1067 PHE 0.033 0.002 PHE C 374 TRP 0.063 0.003 TRP H 47 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.31 (32721) covalent geometry : angle 0.77590 / 0.39 (44535) SS BOND : bond 0.00520 / 0.32 ( 39) SS BOND : angle 1.89835 / 1.36 ( 78) hydrogen bonds : bond 0.06071 / 4.01 ( 812) hydrogen bonds : angle 6.03927 / 4.11 ( 2208) Misc. bond : bond 0.00559 / 0.36 ( 11) link_BETA1-4 : bond 0.00745 / 0.46 ( 15) link_BETA1-4 : angle 2.05005 / 1.14 ( 45) link_BETA1-6 : bond 0.00513 / 0.21 ( 3) link_BETA1-6 : angle 1.48473 / 0.82 ( 9) link_NAG-ASN : bond 0.00822 / 0.46 ( 45) link_NAG-ASN : angle 3.17450 / 2.02 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 171 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7154 (m-70) cc_final: 0.6873 (m-70) REVERT: A 630 THR cc_start: 0.4294 (OUTLIER) cc_final: 0.4011 (t) REVERT: A 855 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.6843 (m-10) REVERT: B 759 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7391 (t80) REVERT: B 878 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 906 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7940 (t80) REVERT: B 1029 MET cc_start: 0.8443 (ttm) cc_final: 0.8131 (ttt) REVERT: C 190 ARG cc_start: 0.7738 (mtt90) cc_final: 0.7433 (mtt90) REVERT: C 403 ARG cc_start: 0.7607 (tpt-90) cc_final: 0.7117 (tpp80) REVERT: C 957 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8282 (tm-30) REVERT: G 46 ARG cc_start: 0.7113 (mpp-170) cc_final: 0.6156 (mmp-170) REVERT: H 45 LEU cc_start: 0.8255 (mp) cc_final: 0.7524 (tp) REVERT: H 102 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.6972 (tpp-160) REVERT: I 48 MET cc_start: 0.3130 (ppp) cc_final: 0.2516 (pmm) REVERT: I 80 TYR cc_start: 0.6484 (m-80) cc_final: 0.5381 (m-80) REVERT: J 57 ASN cc_start: 0.7446 (p0) cc_final: 0.6796 (p0) outliers start: 90 outliers final: 63 residues processed: 243 average time/residue: 0.1847 time to fit residues: 75.3907 Evaluate side-chains 231 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 163 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 130 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 355 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN E 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.137833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092183 restraints weight = 86813.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090891 restraints weight = 57891.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090429 restraints weight = 52526.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.090753 restraints weight = 53768.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091014 restraints weight = 46333.388| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32834 Z= 0.127 Angle : 0.661 13.188 44802 Z= 0.319 Chirality : 0.047 0.433 5208 Planarity : 0.004 0.059 5670 Dihedral : 4.768 35.188 4301 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.08 % Favored : 90.87 % Rotamer: Outliers : 1.99 % Allowed : 16.27 % Favored : 81.74 % 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: -2.14 (0.13), residues: 3954 helix: 0.11 (0.21), residues: 624 sheet: -0.72 (0.19), residues: 753 loop : -2.16 (0.12), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.023 0.001 TYR I 27 PHE 0.039 0.001 PHE C 374 TRP 0.073 0.002 TRP H 47 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (32721) covalent geometry : angle 0.63702 / 0.31 (44535) SS BOND : bond 0.00288 / 0.18 ( 39) SS BOND : angle 1.32548 / 0.95 ( 78) hydrogen bonds : bond 0.04626 / 3.05 ( 812) hydrogen bonds : angle 5.45745 / 3.71 ( 2208) Misc. bond : bond 0.00830 / 0.38 ( 11) link_BETA1-4 : bond 0.00602 / 0.34 ( 15) link_BETA1-4 : angle 1.84033 / 1.02 ( 45) link_BETA1-6 : bond 0.00667 / 0.30 ( 3) link_BETA1-6 : angle 1.08539 / 0.56 ( 9) link_NAG-ASN : bond 0.00592 / 0.38 ( 45) link_NAG-ASN : angle 2.96513 / 1.88 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7677 (m-80) cc_final: 0.7320 (m-10) REVERT: A 146 HIS cc_start: 0.7136 (m-70) cc_final: 0.6854 (m-70) REVERT: A 855 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: B 759 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7506 (t80) REVERT: B 878 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8675 (tt) REVERT: B 906 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7946 (t80) REVERT: C 135 PHE cc_start: 0.7897 (t80) cc_final: 0.7690 (t80) REVERT: C 190 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7190 (mtt90) REVERT: C 403 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7419 (tpp80) REVERT: C 957 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 1107 ARG cc_start: 0.7722 (tpp80) cc_final: 0.7350 (tpp80) REVERT: G 46 ARG cc_start: 0.7107 (mpp-170) cc_final: 0.6226 (mmp-170) REVERT: H 45 LEU cc_start: 0.8296 (mp) cc_final: 0.7595 (tp) REVERT: H 102 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.6976 (tpp-160) REVERT: I 3 GLN cc_start: 0.6767 (mm110) cc_final: 0.4818 (tt0) REVERT: I 48 MET cc_start: 0.3276 (ppp) cc_final: 0.2755 (pmm) REVERT: I 80 TYR cc_start: 0.6459 (m-80) cc_final: 0.5371 (m-80) REVERT: J 57 ASN cc_start: 0.7493 (p0) cc_final: 0.6822 (p0) outliers start: 68 outliers final: 46 residues processed: 235 average time/residue: 0.1891 time to fit residues: 73.8750 Evaluate side-chains 221 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 282 optimal weight: 0.9990 chunk 23 optimal weight: 0.0000 chunk 317 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 300 optimal weight: 1.9990 chunk 328 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 232 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 188 ASN A 901 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090683 restraints weight = 86847.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091082 restraints weight = 61465.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.090613 restraints weight = 47345.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.090949 restraints weight = 47348.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091019 restraints weight = 44526.480| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32834 Z= 0.132 Angle : 0.657 12.967 44802 Z= 0.316 Chirality : 0.047 0.458 5208 Planarity : 0.004 0.059 5670 Dihedral : 4.659 34.664 4301 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.61 % Favored : 90.34 % Rotamer: Outliers : 1.84 % Allowed : 16.68 % Favored : 81.47 % 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: -2.05 (0.13), residues: 3954 helix: 0.23 (0.21), residues: 624 sheet: -0.69 (0.19), residues: 773 loop : -2.12 (0.12), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.024 0.001 TYR B 501 PHE 0.038 0.001 PHE C 374 TRP 0.049 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (32721) covalent geometry : angle 0.63454 / 0.31 (44535) SS BOND : bond 0.00268 / 0.17 ( 39) SS BOND : angle 1.25913 / 0.89 ( 78) hydrogen bonds : bond 0.04533 / 2.99 ( 812) hydrogen bonds : angle 5.36506 / 3.64 ( 2208) Misc. bond : bond 0.00527 / 0.32 ( 11) link_BETA1-4 : bond 0.00566 / 0.32 ( 15) link_BETA1-4 : angle 1.72673 / 0.97 ( 45) link_BETA1-6 : bond 0.00639 / 0.29 ( 3) link_BETA1-6 : angle 1.11508 / 0.60 ( 9) link_NAG-ASN : bond 0.00544 / 0.35 ( 45) link_NAG-ASN : angle 2.91357 / 1.84 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7635 (m-80) cc_final: 0.7319 (m-10) REVERT: A 121 ASN cc_start: 0.7972 (OUTLIER) cc_final: 0.7642 (t0) REVERT: A 146 HIS cc_start: 0.7165 (m-70) cc_final: 0.6906 (m-70) REVERT: A 630 THR cc_start: 0.4402 (OUTLIER) cc_final: 0.4166 (t) REVERT: A 855 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: B 759 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7580 (t80) REVERT: B 878 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 906 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7792 (t80) REVERT: C 135 PHE cc_start: 0.7893 (t80) cc_final: 0.7667 (t80) REVERT: C 190 ARG cc_start: 0.7553 (mtt90) cc_final: 0.7255 (mtt90) REVERT: C 237 ARG cc_start: 0.7298 (ptt-90) cc_final: 0.6990 (ptt-90) REVERT: C 403 ARG cc_start: 0.7697 (tpt-90) cc_final: 0.7420 (tpp80) REVERT: C 957 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8205 (tm-30) REVERT: G 46 ARG cc_start: 0.7103 (mpp-170) cc_final: 0.6236 (mmp-170) REVERT: H 45 LEU cc_start: 0.8257 (mp) cc_final: 0.7581 (tp) REVERT: I 3 GLN cc_start: 0.6781 (mm110) cc_final: 0.4834 (tt0) REVERT: I 48 MET cc_start: 0.3307 (ppp) cc_final: 0.2822 (pmm) REVERT: I 80 TYR cc_start: 0.6475 (m-80) cc_final: 0.5377 (m-80) REVERT: J 57 ASN cc_start: 0.7504 (p0) cc_final: 0.6821 (p0) REVERT: J 70 MET cc_start: 0.5217 (mmp) cc_final: 0.4770 (mpp) outliers start: 63 outliers final: 50 residues processed: 224 average time/residue: 0.1920 time to fit residues: 71.4753 Evaluate side-chains 225 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 19 optimal weight: 0.0070 chunk 55 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 375 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.139806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094415 restraints weight = 85822.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091863 restraints weight = 64585.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092218 restraints weight = 64363.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092474 restraints weight = 64295.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092511 restraints weight = 54507.260| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32834 Z= 0.138 Angle : 0.653 13.231 44802 Z= 0.314 Chirality : 0.047 0.466 5208 Planarity : 0.004 0.059 5670 Dihedral : 4.633 34.121 4301 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.69 % Favored : 90.26 % Rotamer: Outliers : 1.84 % Allowed : 16.80 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3954 helix: 0.29 (0.21), residues: 624 sheet: -0.67 (0.19), residues: 764 loop : -2.12 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.035 0.001 TYR A 266 PHE 0.037 0.001 PHE C 374 TRP 0.049 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (32721) covalent geometry : angle 0.63138 / 0.31 (44535) SS BOND : bond 0.00279 / 0.17 ( 39) SS BOND : angle 1.26639 / 0.89 ( 78) hydrogen bonds : bond 0.04486 / 2.95 ( 812) hydrogen bonds : angle 5.31690 / 3.61 ( 2208) Misc. bond : bond 0.00519 / 0.32 ( 11) link_BETA1-4 : bond 0.00569 / 0.34 ( 15) link_BETA1-4 : angle 1.71378 / 0.96 ( 45) link_BETA1-6 : bond 0.00613 / 0.28 ( 3) link_BETA1-6 : angle 1.10489 / 0.60 ( 9) link_NAG-ASN : bond 0.00540 / 0.34 ( 45) link_NAG-ASN : angle 2.85840 / 1.82 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7908 Ramachandran restraints generated. 3954 Oldfield, 0 Emsley, 3954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 175 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7556 (m-80) cc_final: 0.7329 (m-10) REVERT: A 146 HIS cc_start: 0.7158 (m-70) cc_final: 0.6897 (m-70) REVERT: A 630 THR cc_start: 0.4265 (OUTLIER) cc_final: 0.4020 (t) REVERT: A 855 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: B 759 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 878 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8668 (tt) REVERT: B 906 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.7996 (t80) REVERT: C 135 PHE cc_start: 0.7735 (t80) cc_final: 0.7473 (t80) REVERT: C 190 ARG cc_start: 0.7360 (mtt90) cc_final: 0.7138 (mtt90) REVERT: C 237 ARG cc_start: 0.7061 (ptt-90) cc_final: 0.6782 (ptt-90) REVERT: C 403 ARG cc_start: 0.7638 (tpt-90) cc_final: 0.7430 (tpp80) REVERT: C 957 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 1107 ARG cc_start: 0.7602 (tpp80) cc_final: 0.7287 (tpp80) REVERT: H 45 LEU cc_start: 0.8183 (mp) cc_final: 0.7477 (tp) REVERT: I 3 GLN cc_start: 0.6919 (mm110) cc_final: 0.4908 (tt0) REVERT: I 48 MET cc_start: 0.3358 (ppp) cc_final: 0.2990 (pmm) REVERT: I 80 TYR cc_start: 0.6384 (m-80) cc_final: 0.5272 (m-80) REVERT: J 57 ASN cc_start: 0.7620 (p0) cc_final: 0.6937 (p0) REVERT: J 70 MET cc_start: 0.5106 (mmp) cc_final: 0.4651 (mpp) outliers start: 63 outliers final: 54 residues processed: 225 average time/residue: 0.1896 time to fit residues: 70.7901 Evaluate side-chains 231 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 245 optimal weight: 1.9990 chunk 344 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 203 optimal weight: 0.0870 chunk 278 optimal weight: 7.9990 chunk 36 optimal weight: 0.0060 chunk 29 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.139735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093357 restraints weight = 85804.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091308 restraints weight = 64257.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091927 restraints weight = 55348.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091967 restraints weight = 56235.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092112 restraints weight = 51160.999| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 32834 Z= 0.158 Angle : 0.750 59.181 44802 Z= 0.392 Chirality : 0.049 0.732 5208 Planarity : 0.004 0.059 5670 Dihedral : 4.664 36.743 4301 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.74 % Favored : 90.21 % Rotamer: Outliers : 1.87 % Allowed : 16.68 % Favored : 81.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.13), residues: 3954 helix: 0.29 (0.21), residues: 624 sheet: -0.66 (0.19), residues: 764 loop : -2.12 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 509 TYR 0.028 0.001 TYR A 266 PHE 0.090 0.001 PHE C 374 TRP 0.043 0.002 TRP B 436 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (32721) covalent geometry : angle 0.73175 / 0.39 (44535) SS BOND : bond 0.00264 / 0.17 ( 39) SS BOND : angle 1.23917 / 0.86 ( 78) hydrogen bonds : bond 0.04499 / 2.96 ( 812) hydrogen bonds : angle 5.31652 / 3.61 ( 2208) Misc. bond : bond 0.01037 / 0.44 ( 11) link_BETA1-4 : bond 0.00492 / 0.26 ( 15) link_BETA1-4 : angle 1.78491 / 0.99 ( 45) link_BETA1-6 : bond 0.00610 / 0.27 ( 3) link_BETA1-6 : angle 1.11694 / 0.60 ( 9) link_NAG-ASN : bond 0.00563 / 0.35 ( 45) link_NAG-ASN : angle 2.84790 / 1.81 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5451.31 seconds wall clock time: 95 minutes 20.02 seconds (5720.02 seconds total)