Starting phenix.real_space_refine on Fri Jun 27 20:27:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqy_34039/06_2025/7yqy_34039.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqy_34039/06_2025/7yqy_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_34039/06_2025/7yqy_34039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqy_34039/06_2025/7yqy_34039.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqy_34039/06_2025/7yqy_34039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqy_34039/06_2025/7yqy_34039.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 39 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 dihedrals: 45 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 dihedrals: 48 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.03, per 1000 atoms: 0.60 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: 8.69 Conformation dependent library (CDL) restraints added in 4.2 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: 4.24 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: 12.96 Time building geometry restraints manager: 10.17 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 - 24.81: 19127 24.81 - 49.62: 1018 49.62 - 74.43: 145 74.43 - 99.23: 57 99.23 - 124.04: 23 Dihedral angle restraints: 20370 sinusoidal: 8832 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 20367 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 1144 or resid 1301 through 1313)) selection = (chain 'C' and (resid 25 through 1144 or resid 1301 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: 3.710 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: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.220 Set scattering table: 0.320 Process input model: 73.540 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.240 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 15.466 124.042 12867 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.035 0.002 TRP H 47 HIS 0.004 0.001 HIS A 66 PHE 0.036 0.001 PHE C 374 TYR 0.022 0.001 TYR I 100 ARG 0.006 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 45) link_NAG-ASN : angle 3.26159 ( 135) link_BETA1-4 : bond 0.00576 ( 15) link_BETA1-4 : angle 2.36043 ( 45) hydrogen bonds : bond 0.26799 ( 812) hydrogen bonds : angle 8.99506 ( 2208) link_BETA1-6 : bond 0.00436 ( 3) link_BETA1-6 : angle 1.57349 ( 9) SS BOND : bond 0.00230 ( 39) SS BOND : angle 1.08070 ( 78) covalent geometry : bond 0.00359 (32721) covalent geometry : angle 0.65396 (44535) Misc. bond : bond 0.01509 ( 11) *********************** 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 : 3.519 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: 0.5862 (m-80) REVERT: G 46 ARG cc_start: 0.7344 (mpp-170) cc_final: 0.5880 (mmp-170) REVERT: H 80 TYR cc_start: 0.8176 (m-10) cc_final: 0.7897 (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: 0.4414 time to fit residues: 182.5392 Evaluate side-chains 181 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 3.710 ------------------------------------------------------------------------------- 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 331 optimal weight: 0.0770 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 356 optimal weight: 20.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4189 r_free = 0.4189 target = 0.138728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093006 restraints weight = 86674.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091088 restraints weight = 59549.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091550 restraints weight = 54646.281| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32834 Z= 0.177 Angle : 0.696 13.665 44802 Z= 0.340 Chirality : 0.048 0.508 5208 Planarity : 0.005 0.074 5670 Dihedral : 10.181 110.590 5863 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.61 % Favored : 90.36 % Rotamer: Outliers : 0.73 % Allowed : 7.55 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3954 helix: -0.43 (0.21), residues: 632 sheet: -0.71 (0.18), residues: 820 loop : -2.09 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 47 HIS 0.007 0.001 HIS B 505 PHE 0.037 0.002 PHE C 374 TYR 0.023 0.001 TYR A1067 ARG 0.005 0.000 ARG B 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00632 ( 45) link_NAG-ASN : angle 3.07412 ( 135) link_BETA1-4 : bond 0.00698 ( 15) link_BETA1-4 : angle 2.58863 ( 45) hydrogen bonds : bond 0.06669 ( 812) hydrogen bonds : angle 6.40419 ( 2208) link_BETA1-6 : bond 0.00431 ( 3) link_BETA1-6 : angle 1.38277 ( 9) SS BOND : bond 0.00287 ( 39) SS BOND : angle 1.40676 ( 78) covalent geometry : bond 0.00408 (32721) covalent geometry : angle 0.66983 (44535) Misc. bond : bond 0.00644 ( 11) *********************** 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 224 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 3.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7576 (m-80) cc_final: 0.7111 (m-10) REVERT: A 353 TRP cc_start: 0.4822 (OUTLIER) cc_final: 0.2779 (m-90) REVERT: B 52 GLN cc_start: 0.8280 (tp40) cc_final: 0.8044 (tp40) REVERT: B 1030 SER cc_start: 0.9251 (m) cc_final: 0.8873 (t) REVERT: C 957 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 72 PHE cc_start: 0.6393 (m-80) cc_final: 0.5987 (m-80) REVERT: G 46 ARG cc_start: 0.7175 (mpp-170) cc_final: 0.5850 (mmp-170) REVERT: I 48 MET cc_start: 0.3006 (ppp) cc_final: 0.2642 (ppp) REVERT: I 70 MET cc_start: 0.1211 (ptt) cc_final: 0.0967 (ptt) REVERT: I 80 TYR cc_start: 0.6548 (m-80) cc_final: 0.5453 (m-80) REVERT: J 57 ASN cc_start: 0.7678 (p0) cc_final: 0.7122 (p0) REVERT: J 70 MET cc_start: 0.5168 (mmt) cc_final: 0.4609 (mpp) outliers start: 25 outliers final: 16 residues processed: 218 average time/residue: 0.4316 time to fit residues: 155.1894 Evaluate side-chains 188 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 3.424 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 582 LEU 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 173 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 316 optimal weight: 0.6980 chunk 238 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 240 optimal weight: 0.1980 chunk 271 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 119 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.139861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.093106 restraints weight = 87200.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092640 restraints weight = 59272.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092169 restraints weight = 54292.040| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1377 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= 0.121 Angle : 0.646 12.394 44802 Z= 0.311 Chirality : 0.047 0.475 5208 Planarity : 0.004 0.066 5670 Dihedral : 8.662 106.500 5858 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.83 % Favored : 91.15 % Rotamer: Outliers : 1.23 % Allowed : 10.04 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 3954 helix: -0.07 (0.21), residues: 633 sheet: -0.59 (0.18), residues: 803 loop : -2.07 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 47 HIS 0.007 0.001 HIS B 505 PHE 0.031 0.001 PHE C 374 TYR 0.034 0.001 TYR F 50 ARG 0.009 0.000 ARG I 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 45) link_NAG-ASN : angle 3.11914 ( 135) link_BETA1-4 : bond 0.00592 ( 15) link_BETA1-4 : angle 2.40947 ( 45) hydrogen bonds : bond 0.05395 ( 812) hydrogen bonds : angle 5.78691 ( 2208) link_BETA1-6 : bond 0.00825 ( 3) link_BETA1-6 : angle 1.23819 ( 9) SS BOND : bond 0.00210 ( 39) SS BOND : angle 1.13047 ( 78) covalent geometry : bond 0.00264 (32721) covalent geometry : angle 0.61755 (44535) Misc. bond : bond 0.00486 ( 11) *********************** 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 243 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7632 (m-80) cc_final: 0.7211 (m-10) REVERT: A 100 ILE cc_start: 0.8473 (mm) cc_final: 0.8256 (mp) REVERT: B 52 GLN cc_start: 0.8224 (tp40) cc_final: 0.7954 (tp40) REVERT: B 1030 SER cc_start: 0.9175 (m) cc_final: 0.8927 (t) REVERT: C 237 ARG cc_start: 0.6674 (ptt-90) cc_final: 0.6243 (ptt-90) REVERT: C 957 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8407 (tm-30) REVERT: F 72 PHE cc_start: 0.6493 (m-80) cc_final: 0.6120 (m-80) REVERT: G 46 ARG cc_start: 0.7196 (mpp-170) cc_final: 0.6018 (mmp-170) REVERT: H 29 PHE cc_start: 0.8608 (t80) cc_final: 0.8357 (t80) REVERT: H 45 LEU cc_start: 0.8285 (mp) cc_final: 0.7563 (tp) REVERT: H 48 MET cc_start: 0.6916 (pmm) cc_final: 0.6695 (pmm) REVERT: H 102 ARG cc_start: 0.7678 (tpp-160) cc_final: 0.7134 (tpp-160) REVERT: I 80 TYR cc_start: 0.6509 (m-80) cc_final: 0.5416 (m-80) REVERT: J 57 ASN cc_start: 0.7609 (p0) cc_final: 0.6977 (p0) REVERT: J 70 MET cc_start: 0.5158 (mmt) cc_final: 0.4623 (mpp) outliers start: 42 outliers final: 23 residues processed: 233 average time/residue: 0.6328 time to fit residues: 254.2283 Evaluate side-chains 195 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 4.522 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain C residue 569 ILE 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 308 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 353 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 332 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 544 ASN A 580 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN B 564 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.136951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089769 restraints weight = 86693.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089328 restraints weight = 62336.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.088854 restraints weight = 53086.047| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 32834 Z= 0.233 Angle : 0.721 13.597 44802 Z= 0.350 Chirality : 0.049 0.549 5208 Planarity : 0.004 0.060 5670 Dihedral : 8.322 101.675 5858 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.19 % Favored : 89.78 % Rotamer: Outliers : 2.19 % Allowed : 12.91 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3954 helix: -0.26 (0.21), residues: 638 sheet: -0.76 (0.19), residues: 776 loop : -2.11 (0.12), residues: 2540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP H 47 HIS 0.006 0.001 HIS B 505 PHE 0.030 0.002 PHE C 374 TYR 0.022 0.002 TYR A1067 ARG 0.006 0.001 ARG I 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 45) link_NAG-ASN : angle 3.21839 ( 135) link_BETA1-4 : bond 0.00678 ( 15) link_BETA1-4 : angle 2.31427 ( 45) hydrogen bonds : bond 0.05783 ( 812) hydrogen bonds : angle 5.91001 ( 2208) link_BETA1-6 : bond 0.00552 ( 3) link_BETA1-6 : angle 1.32212 ( 9) SS BOND : bond 0.00343 ( 39) SS BOND : angle 1.42501 ( 78) covalent geometry : bond 0.00547 (32721) covalent geometry : angle 0.69392 (44535) Misc. bond : bond 0.00510 ( 11) *********************** 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 255 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 180 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7638 (m-80) cc_final: 0.7283 (m-10) REVERT: A 630 THR cc_start: 0.4371 (OUTLIER) cc_final: 0.4115 (t) REVERT: A 820 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 855 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.6483 (m-10) REVERT: A 878 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 1002 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7903 (tm-30) REVERT: B 1030 SER cc_start: 0.9299 (m) cc_final: 0.9031 (t) REVERT: C 957 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8395 (tm-30) REVERT: G 46 ARG cc_start: 0.7131 (mpp-170) cc_final: 0.6223 (mmp-170) REVERT: H 45 LEU cc_start: 0.8359 (mp) cc_final: 0.7574 (tp) REVERT: H 48 MET cc_start: 0.6880 (pmm) cc_final: 0.6668 (pmm) REVERT: H 102 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7217 (tpp-160) REVERT: H 122 LEU cc_start: 0.6825 (tt) cc_final: 0.6345 (mt) REVERT: I 48 MET cc_start: 0.2947 (ppp) cc_final: 0.2525 (pmm) REVERT: I 70 MET cc_start: 0.2242 (ptt) cc_final: 0.1781 (ptt) REVERT: I 80 TYR cc_start: 0.6453 (m-80) cc_final: 0.5341 (m-80) REVERT: J 57 ASN cc_start: 0.7546 (p0) cc_final: 0.6891 (p0) REVERT: J 70 MET cc_start: 0.5314 (mmt) cc_final: 0.4943 (mpp) REVERT: J 81 MET cc_start: 0.6844 (tmm) cc_final: 0.6643 (ppp) outliers start: 75 outliers final: 41 residues processed: 242 average time/residue: 0.4069 time to fit residues: 164.6108 Evaluate side-chains 212 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 3.625 ------------------------------------------------------------------------------- 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 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 820 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU 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 65 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 510 VAL 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 90 VAL Chi-restraints excluded: chain C residue 109 THR 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 512 VAL Chi-restraints excluded: chain C residue 569 ILE 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 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 278 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 140 optimal weight: 0.0670 chunk 60 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 287 optimal weight: 1.9990 chunk 370 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 337 optimal weight: 0.2980 overall best weight: 1.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.138303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092482 restraints weight = 86831.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090207 restraints weight = 63876.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.090625 restraints weight = 62164.836| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32834 Z= 0.133 Angle : 0.649 12.024 44802 Z= 0.313 Chirality : 0.047 0.518 5208 Planarity : 0.004 0.059 5670 Dihedral : 7.921 97.854 5858 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.05 % Favored : 90.92 % Rotamer: Outliers : 1.96 % Allowed : 13.96 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.13), residues: 3954 helix: 0.06 (0.21), residues: 629 sheet: -0.64 (0.18), residues: 818 loop : -2.14 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP H 47 HIS 0.006 0.001 HIS B 505 PHE 0.029 0.001 PHE C 374 TYR 0.020 0.001 TYR F 50 ARG 0.005 0.000 ARG I 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 45) link_NAG-ASN : angle 3.07893 ( 135) link_BETA1-4 : bond 0.00691 ( 15) link_BETA1-4 : angle 2.23670 ( 45) hydrogen bonds : bond 0.04943 ( 812) hydrogen bonds : angle 5.55238 ( 2208) link_BETA1-6 : bond 0.00859 ( 3) link_BETA1-6 : angle 1.27152 ( 9) SS BOND : bond 0.00632 ( 39) SS BOND : angle 1.21808 ( 78) covalent geometry : bond 0.00297 (32721) covalent geometry : angle 0.62259 (44535) Misc. bond : bond 0.00602 ( 11) *********************** 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 249 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7689 (m-80) cc_final: 0.7326 (m-10) REVERT: A 630 THR cc_start: 0.4230 (OUTLIER) cc_final: 0.3967 (t) REVERT: A 855 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: B 759 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7439 (t80) REVERT: B 1030 SER cc_start: 0.9210 (m) cc_final: 0.8961 (t) REVERT: C 957 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8294 (tm-30) REVERT: G 46 ARG cc_start: 0.7120 (mpp-170) cc_final: 0.6238 (mmp-170) REVERT: H 29 PHE cc_start: 0.8654 (t80) cc_final: 0.8369 (t80) REVERT: H 45 LEU cc_start: 0.8348 (mp) cc_final: 0.7577 (tp) REVERT: H 48 MET cc_start: 0.6691 (pmm) cc_final: 0.6488 (pmm) REVERT: H 80 TYR cc_start: 0.7970 (m-10) cc_final: 0.7688 (m-10) REVERT: H 102 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7289 (tpp-160) REVERT: H 122 LEU cc_start: 0.6759 (tt) cc_final: 0.6289 (mt) REVERT: I 80 TYR cc_start: 0.6541 (m-80) cc_final: 0.5429 (m-80) REVERT: J 57 ASN cc_start: 0.7476 (p0) cc_final: 0.6801 (p0) REVERT: J 70 MET cc_start: 0.5259 (mmt) cc_final: 0.4906 (mpp) outliers start: 67 outliers final: 36 residues processed: 237 average time/residue: 0.4103 time to fit residues: 161.5970 Evaluate side-chains 206 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 3.512 ------------------------------------------------------------------------------- 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 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 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 90 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 510 VAL 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 931 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1122 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 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 902 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 56 optimal weight: 9.9990 chunk 329 optimal weight: 40.0000 chunk 359 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4182 r_free = 0.4182 target = 0.142866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094599 restraints weight = 84697.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092890 restraints weight = 61045.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093117 restraints weight = 56976.571| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32834 Z= 0.199 Angle : 0.692 12.293 44802 Z= 0.334 Chirality : 0.048 0.546 5208 Planarity : 0.004 0.058 5670 Dihedral : 7.830 90.715 5858 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.17 % Favored : 89.81 % Rotamer: Outliers : 2.43 % Allowed : 14.46 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3954 helix: -0.03 (0.21), residues: 635 sheet: -0.71 (0.19), residues: 786 loop : -2.16 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP H 47 HIS 0.005 0.001 HIS B 505 PHE 0.037 0.002 PHE C 374 TYR 0.021 0.002 TYR A1067 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 45) link_NAG-ASN : angle 3.17465 ( 135) link_BETA1-4 : bond 0.00631 ( 15) link_BETA1-4 : angle 2.13618 ( 45) hydrogen bonds : bond 0.05212 ( 812) hydrogen bonds : angle 5.65781 ( 2208) link_BETA1-6 : bond 0.00563 ( 3) link_BETA1-6 : angle 1.29307 ( 9) SS BOND : bond 0.00334 ( 39) SS BOND : angle 1.68804 ( 78) covalent geometry : bond 0.00463 (32721) covalent geometry : angle 0.66473 (44535) Misc. bond : bond 0.00607 ( 11) *********************** 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 261 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 178 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7778 (m-80) cc_final: 0.7393 (m-10) REVERT: A 630 THR cc_start: 0.4202 (OUTLIER) cc_final: 0.3955 (t) REVERT: A 855 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6571 (m-10) REVERT: B 759 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 878 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8706 (tt) REVERT: B 906 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 1030 SER cc_start: 0.9264 (m) cc_final: 0.8986 (t) REVERT: C 957 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8348 (tm-30) REVERT: G 46 ARG cc_start: 0.7029 (mpp-170) cc_final: 0.6052 (mmp-170) REVERT: H 29 PHE cc_start: 0.8694 (t80) cc_final: 0.8376 (t80) REVERT: H 45 LEU cc_start: 0.8311 (mp) cc_final: 0.7550 (tp) REVERT: H 48 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6478 (pmm) REVERT: H 102 ARG cc_start: 0.7689 (tpp-160) cc_final: 0.7149 (tpp-160) REVERT: I 48 MET cc_start: 0.2959 (ppp) cc_final: 0.2091 (pmm) REVERT: I 80 TYR cc_start: 0.6469 (m-80) cc_final: 0.5378 (m-80) REVERT: J 57 ASN cc_start: 0.7492 (p0) cc_final: 0.6785 (p0) REVERT: J 70 MET cc_start: 0.5293 (mmt) cc_final: 0.4899 (mpp) outliers start: 83 outliers final: 51 residues processed: 248 average time/residue: 0.3937 time to fit residues: 166.1175 Evaluate side-chains 220 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 163 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE 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 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 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 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 390 LEU Chi-restraints excluded: chain B residue 510 VAL 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 1123 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 144 TYR 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 584 ILE 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 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 F residue 14 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain J residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 138 optimal weight: 5.9990 chunk 342 optimal weight: 0.0270 chunk 162 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 65 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.138469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091666 restraints weight = 86970.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.091215 restraints weight = 61131.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091052 restraints weight = 48510.713| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32834 Z= 0.121 Angle : 0.650 13.633 44802 Z= 0.311 Chirality : 0.047 0.515 5208 Planarity : 0.004 0.059 5670 Dihedral : 7.474 80.856 5858 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.95 % Favored : 91.02 % Rotamer: Outliers : 1.96 % Allowed : 15.28 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 3954 helix: 0.25 (0.21), residues: 629 sheet: -0.65 (0.18), residues: 801 loop : -2.14 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP H 47 HIS 0.005 0.000 HIS B 505 PHE 0.037 0.001 PHE C 374 TYR 0.026 0.001 TYR F 50 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 45) link_NAG-ASN : angle 3.15032 ( 135) link_BETA1-4 : bond 0.00573 ( 15) link_BETA1-4 : angle 2.05784 ( 45) hydrogen bonds : bond 0.04520 ( 812) hydrogen bonds : angle 5.38801 ( 2208) link_BETA1-6 : bond 0.00649 ( 3) link_BETA1-6 : angle 1.14825 ( 9) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.42443 ( 78) covalent geometry : bond 0.00273 (32721) covalent geometry : angle 0.62237 (44535) Misc. bond : bond 0.00565 ( 11) *********************** 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 249 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 182 time to evaluate : 3.743 Fit side-chains revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7567 (m-80) cc_final: 0.7292 (m-10) REVERT: A 630 THR cc_start: 0.4043 (OUTLIER) cc_final: 0.3803 (t) REVERT: A 855 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6526 (m-10) REVERT: B 759 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7325 (t80) REVERT: B 906 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7956 (t80) REVERT: B 1030 SER cc_start: 0.9190 (m) cc_final: 0.8981 (t) REVERT: C 237 ARG cc_start: 0.7035 (ptt-90) cc_final: 0.6619 (ptt-90) REVERT: C 957 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8293 (tm-30) REVERT: H 29 PHE cc_start: 0.8621 (t80) cc_final: 0.8379 (t80) REVERT: H 45 LEU cc_start: 0.8281 (mp) cc_final: 0.7530 (tp) REVERT: H 102 ARG cc_start: 0.7704 (tpp-160) cc_final: 0.7258 (tpp-160) REVERT: I 48 MET cc_start: 0.3299 (ppp) cc_final: 0.2719 (pmm) REVERT: I 80 TYR cc_start: 0.6398 (m-80) cc_final: 0.5331 (m-80) REVERT: J 57 ASN cc_start: 0.7537 (p0) cc_final: 0.6825 (p0) REVERT: J 70 MET cc_start: 0.5356 (mmt) cc_final: 0.4986 (mpp) outliers start: 67 outliers final: 45 residues processed: 236 average time/residue: 0.4016 time to fit residues: 159.6956 Evaluate side-chains 218 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 3.273 ------------------------------------------------------------------------------- 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 649 CYS 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 874 THR 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 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 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 510 VAL Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 620 VAL 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 1122 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 90 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 620 VAL 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 63 LYS Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 375 optimal weight: 0.5980 chunk 336 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 391 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN H 43 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.135364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089616 restraints weight = 87609.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086965 restraints weight = 61879.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087158 restraints weight = 58536.789| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 32834 Z= 0.283 Angle : 0.772 14.984 44802 Z= 0.375 Chirality : 0.051 0.575 5208 Planarity : 0.005 0.059 5670 Dihedral : 7.793 72.124 5858 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.48 % Favored : 88.49 % Rotamer: Outliers : 2.37 % Allowed : 15.72 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3954 helix: -0.16 (0.21), residues: 638 sheet: -0.80 (0.19), residues: 749 loop : -2.20 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 436 HIS 0.004 0.001 HIS C1058 PHE 0.039 0.002 PHE C 374 TYR 0.026 0.002 TYR F 50 ARG 0.006 0.001 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 45) link_NAG-ASN : angle 3.44523 ( 135) link_BETA1-4 : bond 0.00682 ( 15) link_BETA1-4 : angle 2.13196 ( 45) hydrogen bonds : bond 0.05691 ( 812) hydrogen bonds : angle 5.84534 ( 2208) link_BETA1-6 : bond 0.00468 ( 3) link_BETA1-6 : angle 1.41913 ( 9) SS BOND : bond 0.00415 ( 39) SS BOND : angle 1.74821 ( 78) covalent geometry : bond 0.00670 (32721) covalent geometry : angle 0.74389 (44535) Misc. bond : bond 0.00541 ( 11) *********************** 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 260 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 179 time to evaluate : 4.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7722 (m-80) cc_final: 0.7375 (m-10) REVERT: A 146 HIS cc_start: 0.7301 (m-70) cc_final: 0.7038 (m-70) REVERT: A 630 THR cc_start: 0.4611 (OUTLIER) cc_final: 0.4348 (t) REVERT: A 855 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.6483 (m-10) REVERT: B 759 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7448 (t80) REVERT: B 878 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8730 (tt) REVERT: B 906 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7931 (t80) REVERT: B 1030 SER cc_start: 0.9234 (m) cc_final: 0.8926 (t) REVERT: C 957 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8288 (tm-30) REVERT: G 46 ARG cc_start: 0.6297 (mtm-85) cc_final: 0.5666 (mmp-170) REVERT: H 29 PHE cc_start: 0.8751 (t80) cc_final: 0.8514 (t80) REVERT: H 47 TRP cc_start: 0.8020 (t60) cc_final: 0.7674 (t60) REVERT: H 102 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7321 (tpp-160) REVERT: I 48 MET cc_start: 0.3324 (ppp) cc_final: 0.2735 (pmm) REVERT: I 80 TYR cc_start: 0.6440 (m-80) cc_final: 0.5396 (m-80) REVERT: I 102 ARG cc_start: 0.4388 (ttp-170) cc_final: 0.3765 (tmm160) REVERT: J 57 ASN cc_start: 0.7466 (p0) cc_final: 0.6765 (p0) REVERT: E 29 VAL cc_start: -0.2052 (OUTLIER) cc_final: -0.2305 (m) outliers start: 81 outliers final: 56 residues processed: 245 average time/residue: 0.4398 time to fit residues: 181.1852 Evaluate side-chains 233 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 LEU 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 630 THR Chi-restraints excluded: chain A residue 649 CYS 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 1104 VAL Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 65 PHE 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 510 VAL 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 90 VAL Chi-restraints excluded: chain C residue 109 THR 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 433 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 718 PHE Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 883 THR 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 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 68 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 303 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 309 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 260 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 180 optimal weight: 0.1980 chunk 239 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 644 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4186 r_free = 0.4186 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090297 restraints weight = 86688.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090520 restraints weight = 64474.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090480 restraints weight = 51696.890| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2476 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 : 0.668 13.131 44802 Z= 0.319 Chirality : 0.047 0.520 5208 Planarity : 0.004 0.060 5670 Dihedral : 7.331 62.774 5858 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 1.84 % Allowed : 16.56 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3954 helix: 0.25 (0.21), residues: 624 sheet: -0.72 (0.19), residues: 782 loop : -2.13 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 PHE 0.049 0.001 PHE C 374 TYR 0.024 0.001 TYR F 50 ARG 0.005 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 45) link_NAG-ASN : angle 3.16225 ( 135) link_BETA1-4 : bond 0.00573 ( 15) link_BETA1-4 : angle 2.08938 ( 45) hydrogen bonds : bond 0.04425 ( 812) hydrogen bonds : angle 5.34892 ( 2208) link_BETA1-6 : bond 0.00645 ( 3) link_BETA1-6 : angle 1.09835 ( 9) SS BOND : bond 0.00340 ( 39) SS BOND : angle 1.19173 ( 78) covalent geometry : bond 0.00263 (32721) covalent geometry : angle 0.64096 (44535) Misc. bond : bond 0.00619 ( 11) *********************** 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 241 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 178 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7581 (m-80) cc_final: 0.7260 (m-10) REVERT: A 146 HIS cc_start: 0.7084 (m-70) cc_final: 0.6833 (m-70) REVERT: A 855 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6467 (m-10) REVERT: B 759 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 878 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8630 (tt) REVERT: B 906 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.7848 (t80) REVERT: C 135 PHE cc_start: 0.7787 (t80) cc_final: 0.7568 (t80) REVERT: C 237 ARG cc_start: 0.7222 (ptt-90) cc_final: 0.6922 (ptt-90) REVERT: C 957 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8151 (tm-30) REVERT: H 102 ARG cc_start: 0.7790 (tpp-160) cc_final: 0.7343 (tpp-160) REVERT: I 48 MET cc_start: 0.3382 (ppp) cc_final: 0.3110 (pmm) REVERT: I 70 MET cc_start: 0.1857 (ptt) cc_final: -0.0504 (ptp) REVERT: I 80 TYR cc_start: 0.6415 (m-80) cc_final: 0.5331 (m-80) REVERT: I 102 ARG cc_start: 0.4074 (ttp-170) cc_final: 0.3169 (tmm160) REVERT: J 57 ASN cc_start: 0.7539 (p0) cc_final: 0.6841 (p0) outliers start: 63 outliers final: 48 residues processed: 229 average time/residue: 0.4279 time to fit residues: 163.0980 Evaluate side-chains 221 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE 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 212 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 649 CYS 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 874 THR 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 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 275 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 541 PHE 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 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 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 1122 VAL 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 68 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 110 LEU 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 264 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 220 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 217 optimal weight: 0.5980 chunk 266 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 chunk 42 optimal weight: 0.0970 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 188 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.145559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096830 restraints weight = 83946.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095362 restraints weight = 60258.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096057 restraints weight = 56306.689| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.136 32834 Z= 0.151 Angle : 0.783 59.198 44802 Z= 0.405 Chirality : 0.049 0.626 5208 Planarity : 0.004 0.127 5670 Dihedral : 7.350 62.707 5858 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.23 % Favored : 90.72 % Rotamer: Outliers : 1.61 % Allowed : 16.68 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3954 helix: 0.26 (0.21), residues: 624 sheet: -0.71 (0.19), residues: 780 loop : -2.13 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 PHE 0.052 0.001 PHE C 374 TYR 0.024 0.001 TYR F 50 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00953 ( 45) link_NAG-ASN : angle 3.14110 ( 135) link_BETA1-4 : bond 0.00522 ( 15) link_BETA1-4 : angle 2.16588 ( 45) hydrogen bonds : bond 0.04453 ( 812) hydrogen bonds : angle 5.34429 ( 2208) link_BETA1-6 : bond 0.00495 ( 3) link_BETA1-6 : angle 1.11222 ( 9) SS BOND : bond 0.00313 ( 39) SS BOND : angle 1.19162 ( 78) covalent geometry : bond 0.00327 (32721) covalent geometry : angle 0.76076 (44535) Misc. bond : bond 0.01867 ( 11) ********************** 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 224 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7739 (m-80) cc_final: 0.7394 (m-10) REVERT: A 146 HIS cc_start: 0.7340 (m-70) cc_final: 0.7131 (m-70) REVERT: A 855 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6485 (m-10) REVERT: B 759 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7450 (t80) REVERT: B 878 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 906 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.7977 (t80) REVERT: C 135 PHE cc_start: 0.7840 (t80) cc_final: 0.7603 (t80) REVERT: C 957 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8148 (tm-30) REVERT: H 48 MET cc_start: 0.6107 (pmm) cc_final: 0.5812 (pmm) REVERT: H 102 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7348 (tpp-160) REVERT: I 48 MET cc_start: 0.3326 (ppp) cc_final: 0.3062 (pmm) REVERT: I 70 MET cc_start: 0.2702 (ptt) cc_final: 0.0370 (ptp) REVERT: I 80 TYR cc_start: 0.6447 (m-80) cc_final: 0.5426 (m-80) REVERT: J 57 ASN cc_start: 0.7333 (p0) cc_final: 0.6627 (p0) outliers start: 55 outliers final: 48 residues processed: 212 average time/residue: 0.4264 time to fit residues: 150.3966 Evaluate side-chains 222 residues out of total 3441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 649 CYS 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 874 THR Chi-restraints excluded: chain A residue 1029 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 200 TYR Chi-restraints excluded: chain B residue 275 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 541 PHE 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 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 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 1122 VAL 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 68 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 110 LEU 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 18 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 388 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 75 optimal weight: 0.1980 chunk 312 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 chunk 224 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4205 r_free = 0.4205 target = 0.145563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096865 restraints weight = 83310.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096218 restraints weight = 57315.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096121 restraints weight = 51193.149| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 32834 Z= 0.191 Angle : 0.780 59.198 44802 Z= 0.404 Chirality : 0.049 0.626 5208 Planarity : 0.004 0.127 5670 Dihedral : 7.350 62.707 5858 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.23 % Favored : 90.72 % Rotamer: Outliers : 1.52 % Allowed : 16.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3954 helix: 0.26 (0.21), residues: 624 sheet: -0.71 (0.19), residues: 780 loop : -2.13 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 436 HIS 0.005 0.001 HIS B 505 PHE 0.052 0.001 PHE C 374 TYR 0.024 0.001 TYR F 50 ARG 0.004 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.03216 ( 45) link_NAG-ASN : angle 2.94917 ( 135) link_BETA1-4 : bond 0.00522 ( 15) link_BETA1-4 : angle 2.16588 ( 45) hydrogen bonds : bond 0.04453 ( 812) hydrogen bonds : angle 5.34429 ( 2208) link_BETA1-6 : bond 0.00495 ( 3) link_BETA1-6 : angle 1.11222 ( 9) SS BOND : bond 0.00313 ( 39) SS BOND : angle 1.19162 ( 78) covalent geometry : bond 0.00327 (32721) covalent geometry : angle 0.76076 (44535) Misc. bond : bond 0.05894 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11071.77 seconds wall clock time: 196 minutes 30.44 seconds (11790.44 seconds total)