Starting phenix.real_space_refine on Fri Mar 6 03:56:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nda_12281/03_2026/7nda_12281.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 121 5.16 5 C 17601 2.51 5 N 4532 2.21 5 O 5467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27721 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7845 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 49, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7833 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 49, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7896 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1630 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.23, per 1000 atoms: 0.22 Number of scatterers: 27721 At special positions: 0 Unit cell: (138.61, 153.55, 211.65, 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 121 16.00 O 5467 8.00 N 4532 7.00 C 17601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN H 102 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6458 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 56 sheets defined 23.3% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.379A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 removed outlier: 3.676A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.433A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.194A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.325A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.621A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.564A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.927A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.552A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.110A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.419A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.590A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.554A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.516A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.921A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.524A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.121A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.657A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.516A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.841A pdb=" N GLY H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.680A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.334A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.080A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.530A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.509A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.779A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.443A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.808A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.392A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.178A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.945A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.061A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.385A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.846A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.498A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.696A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.771A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.771A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.592A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.183A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.904A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.966A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.446A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.331A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.928A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.928A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.424A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.424A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.103A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.695A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.118A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.118A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.599A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.559A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.887A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.905A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 154 through 155 1175 hydrogen bonds defined for protein. 3204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.49 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8806 1.34 - 1.46: 7037 1.46 - 1.58: 12333 1.58 - 1.71: 0 1.71 - 1.83: 149 Bond restraints: 28325 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 ... (remaining 28320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 37917 2.14 - 4.28: 571 4.28 - 6.42: 47 6.42 - 8.56: 4 8.56 - 10.70: 3 Bond angle restraints: 38542 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.89 -10.49 2.30e+00 1.89e-01 2.08e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 124.06 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CA TYR A 904 " pdb=" CB TYR A 904 " pdb=" CG TYR A 904 " ideal model delta sigma weight residual 113.90 120.31 -6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA TYR B 904 " pdb=" CB TYR B 904 " pdb=" CG TYR B 904 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 119.88 -5.98 1.80e+00 3.09e-01 1.11e+01 ... (remaining 38537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16824 17.98 - 35.97: 644 35.97 - 53.95: 149 53.95 - 71.93: 60 71.93 - 89.92: 23 Dihedral angle restraints: 17700 sinusoidal: 7670 harmonic: 10030 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.12 76.12 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.11 76.11 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -161.68 75.68 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 17697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3329 0.045 - 0.090: 855 0.090 - 0.135: 376 0.135 - 0.180: 16 0.180 - 0.226: 2 Chirality restraints: 4578 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 4575 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 954 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B 954 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN B 954 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 954 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN C 954 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN C 954 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 955 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C ALA C 958 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA C 958 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 959 " -0.018 2.00e-02 2.50e+03 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 233 2.62 - 3.19: 23850 3.19 - 3.76: 41821 3.76 - 4.33: 60278 4.33 - 4.90: 99195 Nonbonded interactions: 225377 Sorted by model distance: nonbonded pdb=" OE1 GLU L 106 " pdb=" OH TYR L 174 " model vdw 2.051 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.189 3.040 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.190 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.191 3.040 nonbonded pdb=" OD2 ASP L 171 " pdb=" OG1 THR L 173 " model vdw 2.201 3.040 ... (remaining 225372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 1310)) selection = (chain 'B' and (resid 27 through 827 or resid 853 through 1310)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 827 or resid 853 throu \ gh 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.260 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.043 28432 Z= 0.187 Angle : 0.637 10.697 38819 Z= 0.332 Chirality : 0.046 0.226 4578 Planarity : 0.004 0.064 4899 Dihedral : 11.131 89.915 11110 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.38 % Favored : 95.29 % Rotamer: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3398 helix: 0.66 (0.19), residues: 679 sheet: 0.42 (0.16), residues: 902 loop : -0.63 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.022 0.001 TYR A 789 PHE 0.018 0.001 PHE C 515 TRP 0.021 0.001 TRP A 886 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00389 (28325) covalent geometry : angle 0.62862 (38542) SS BOND : bond 0.00381 ( 44) SS BOND : angle 1.45067 ( 88) hydrogen bonds : bond 0.10811 ( 1120) hydrogen bonds : angle 7.30490 ( 3204) link_BETA1-4 : bond 0.00238 ( 15) link_BETA1-4 : angle 0.85911 ( 45) link_BETA1-6 : bond 0.00346 ( 1) link_BETA1-6 : angle 1.33039 ( 3) link_NAG-ASN : bond 0.00136 ( 47) link_NAG-ASN : angle 1.42593 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 556 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8403 (m-80) cc_final: 0.8168 (m-10) REVERT: A 192 PHE cc_start: 0.8606 (m-80) cc_final: 0.8265 (m-10) REVERT: A 270 LEU cc_start: 0.8594 (mt) cc_final: 0.8380 (mp) REVERT: A 398 ASP cc_start: 0.7812 (m-30) cc_final: 0.7516 (m-30) REVERT: A 549 THR cc_start: 0.8440 (m) cc_final: 0.8212 (m) REVERT: A 565 PHE cc_start: 0.7494 (m-80) cc_final: 0.7137 (m-10) REVERT: A 745 ASP cc_start: 0.7220 (m-30) cc_final: 0.6755 (t0) REVERT: A 779 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8262 (tp40) REVERT: A 979 ASP cc_start: 0.7763 (m-30) cc_final: 0.7487 (t0) REVERT: B 41 LYS cc_start: 0.8102 (mttp) cc_final: 0.7532 (mtpt) REVERT: C 42 VAL cc_start: 0.9330 (t) cc_final: 0.9056 (t) REVERT: C 49 HIS cc_start: 0.7591 (t70) cc_final: 0.7325 (t70) REVERT: C 104 TRP cc_start: 0.5850 (m-90) cc_final: 0.5181 (m-90) REVERT: C 223 LEU cc_start: 0.8519 (mp) cc_final: 0.8048 (mp) REVERT: C 266 TYR cc_start: 0.7086 (m-80) cc_final: 0.6138 (m-80) REVERT: C 354 ASN cc_start: 0.8621 (t0) cc_final: 0.8197 (t0) REVERT: C 490 PHE cc_start: 0.8830 (t80) cc_final: 0.8595 (t80) REVERT: C 1101 HIS cc_start: 0.7196 (m90) cc_final: 0.6956 (m-70) REVERT: H 36 TRP cc_start: 0.5795 (m100) cc_final: 0.5593 (m100) REVERT: L 50 TYR cc_start: 0.7859 (p90) cc_final: 0.6877 (p90) REVERT: L 63 PHE cc_start: 0.8361 (m-80) cc_final: 0.7812 (m-80) outliers start: 9 outliers final: 5 residues processed: 565 average time/residue: 0.2064 time to fit residues: 180.0164 Evaluate side-chains 317 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 311 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 849 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 907 ASN A 913 GLN A 935 GLN A 955 ASN B 125 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 955 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.170725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103009 restraints weight = 52488.047| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.59 r_work: 0.3154 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28432 Z= 0.177 Angle : 0.624 12.081 38819 Z= 0.323 Chirality : 0.045 0.220 4578 Planarity : 0.004 0.069 4899 Dihedral : 6.346 59.689 5012 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.30 % Favored : 97.62 % Rotamer: Outliers : 1.33 % Allowed : 8.23 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3398 helix: 1.29 (0.20), residues: 687 sheet: 0.52 (0.16), residues: 912 loop : -0.44 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 34 TYR 0.026 0.002 TYR C 453 PHE 0.023 0.002 PHE C 55 TRP 0.023 0.002 TRP B 353 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00412 (28325) covalent geometry : angle 0.61211 (38542) SS BOND : bond 0.00389 ( 44) SS BOND : angle 1.71434 ( 88) hydrogen bonds : bond 0.04229 ( 1120) hydrogen bonds : angle 6.04249 ( 3204) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.08223 ( 45) link_BETA1-6 : bond 0.00280 ( 1) link_BETA1-6 : angle 1.39206 ( 3) link_NAG-ASN : bond 0.00272 ( 47) link_NAG-ASN : angle 1.54822 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 343 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.8387 (m-80) cc_final: 0.8164 (m-10) REVERT: A 192 PHE cc_start: 0.8653 (m-80) cc_final: 0.8381 (m-10) REVERT: A 270 LEU cc_start: 0.8635 (mt) cc_final: 0.8322 (mp) REVERT: A 271 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8174 (mm110) REVERT: A 342 PHE cc_start: 0.9357 (m-80) cc_final: 0.9042 (m-80) REVERT: A 451 TYR cc_start: 0.6693 (m-80) cc_final: 0.5978 (m-80) REVERT: A 740 MET cc_start: 0.8974 (ttt) cc_final: 0.8754 (ttp) REVERT: A 745 ASP cc_start: 0.8077 (m-30) cc_final: 0.7227 (t0) REVERT: A 979 ASP cc_start: 0.8086 (m-30) cc_final: 0.7784 (t0) REVERT: A 995 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8369 (ttm170) REVERT: B 41 LYS cc_start: 0.8257 (mttp) cc_final: 0.7796 (mtpt) REVERT: B 191 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 398 ASP cc_start: 0.8662 (m-30) cc_final: 0.7139 (p0) REVERT: B 755 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7526 (mm-40) REVERT: B 988 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8835 (mp0) REVERT: C 40 ASP cc_start: 0.8437 (p0) cc_final: 0.8231 (p0) REVERT: C 49 HIS cc_start: 0.7809 (t70) cc_final: 0.7376 (t-170) REVERT: C 86 PHE cc_start: 0.8125 (t80) cc_final: 0.7324 (t80) REVERT: C 104 TRP cc_start: 0.6067 (m-90) cc_final: 0.5482 (m-90) REVERT: C 194 PHE cc_start: 0.8694 (m-80) cc_final: 0.8459 (m-10) REVERT: C 223 LEU cc_start: 0.8682 (mp) cc_final: 0.8112 (mp) REVERT: C 266 TYR cc_start: 0.7253 (m-80) cc_final: 0.6434 (m-80) REVERT: C 269 TYR cc_start: 0.5784 (m-80) cc_final: 0.5385 (m-80) REVERT: C 354 ASN cc_start: 0.8280 (t0) cc_final: 0.7762 (t0) REVERT: C 424 LYS cc_start: 0.8272 (tptt) cc_final: 0.8071 (tppt) REVERT: C 461 LEU cc_start: 0.8794 (mm) cc_final: 0.8322 (mm) REVERT: C 466 ARG cc_start: 0.7985 (ttm110) cc_final: 0.6474 (ptp-170) REVERT: C 490 PHE cc_start: 0.8999 (t80) cc_final: 0.8614 (t80) REVERT: C 955 ASN cc_start: 0.8329 (m110) cc_final: 0.8118 (m-40) REVERT: C 994 ASP cc_start: 0.8191 (m-30) cc_final: 0.7942 (m-30) REVERT: C 1101 HIS cc_start: 0.8256 (m90) cc_final: 0.7752 (m-70) REVERT: H 36 TRP cc_start: 0.6260 (m100) cc_final: 0.5649 (m100) REVERT: H 48 ILE cc_start: 0.8348 (mt) cc_final: 0.8107 (mp) REVERT: H 74 MET cc_start: 0.8556 (mpp) cc_final: 0.7824 (mpp) REVERT: H 108 ASP cc_start: 0.8895 (p0) cc_final: 0.8666 (p0) REVERT: H 186 TYR cc_start: 0.8585 (m-80) cc_final: 0.8334 (m-80) REVERT: L 4 MET cc_start: 0.4527 (mtp) cc_final: 0.3890 (mtp) REVERT: L 63 PHE cc_start: 0.8989 (m-80) cc_final: 0.8031 (m-80) REVERT: L 72 PHE cc_start: 0.8986 (m-80) cc_final: 0.7834 (t80) outliers start: 40 outliers final: 25 residues processed: 374 average time/residue: 0.1973 time to fit residues: 115.6239 Evaluate side-chains 314 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 288 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain L residue 109 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 334 optimal weight: 0.7980 chunk 311 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 388 ASN A 907 ASN B 207 HIS B1002 GLN C 360 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN L 148 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.171035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.099922 restraints weight = 52825.692| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.56 r_work: 0.3086 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 28432 Z= 0.243 Angle : 0.648 10.815 38819 Z= 0.332 Chirality : 0.046 0.188 4578 Planarity : 0.004 0.068 4899 Dihedral : 5.732 59.166 5004 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.00 % Favored : 96.91 % Rotamer: Outliers : 2.03 % Allowed : 9.43 % Favored : 88.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3398 helix: 1.15 (0.20), residues: 687 sheet: 0.52 (0.17), residues: 918 loop : -0.44 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.037 0.002 TYR B 904 PHE 0.035 0.002 PHE B 342 TRP 0.034 0.002 TRP A 436 HIS 0.010 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00568 (28325) covalent geometry : angle 0.63668 (38542) SS BOND : bond 0.00368 ( 44) SS BOND : angle 1.63171 ( 88) hydrogen bonds : bond 0.04306 ( 1120) hydrogen bonds : angle 5.90017 ( 3204) link_BETA1-4 : bond 0.00225 ( 15) link_BETA1-4 : angle 1.13729 ( 45) link_BETA1-6 : bond 0.00359 ( 1) link_BETA1-6 : angle 1.41827 ( 3) link_NAG-ASN : bond 0.00833 ( 47) link_NAG-ASN : angle 1.61135 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8567 (t70) cc_final: 0.8300 (t-170) REVERT: A 192 PHE cc_start: 0.8799 (m-80) cc_final: 0.8442 (m-10) REVERT: A 202 LYS cc_start: 0.9059 (mttm) cc_final: 0.8729 (mtpm) REVERT: A 270 LEU cc_start: 0.8778 (mt) cc_final: 0.8246 (mp) REVERT: A 271 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8238 (mm110) REVERT: A 342 PHE cc_start: 0.9390 (m-80) cc_final: 0.9092 (m-80) REVERT: A 451 TYR cc_start: 0.6603 (m-80) cc_final: 0.6184 (m-80) REVERT: A 511 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 581 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (p) REVERT: A 740 MET cc_start: 0.9139 (ttt) cc_final: 0.8938 (ttp) REVERT: A 979 ASP cc_start: 0.8141 (m-30) cc_final: 0.7845 (t0) REVERT: A 995 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8393 (ttm110) REVERT: B 41 LYS cc_start: 0.8286 (mttp) cc_final: 0.7631 (mtpt) REVERT: B 88 ASP cc_start: 0.8864 (m-30) cc_final: 0.8460 (p0) REVERT: B 191 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 231 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 329 PHE cc_start: 0.8743 (m-80) cc_final: 0.8538 (m-10) REVERT: B 755 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7646 (mm-40) REVERT: B 985 ASP cc_start: 0.8226 (p0) cc_final: 0.7528 (p0) REVERT: B 988 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8846 (mp0) REVERT: C 49 HIS cc_start: 0.7895 (t70) cc_final: 0.7495 (t-170) REVERT: C 86 PHE cc_start: 0.8228 (t80) cc_final: 0.7726 (t80) REVERT: C 104 TRP cc_start: 0.6299 (m-90) cc_final: 0.5978 (m-90) REVERT: C 223 LEU cc_start: 0.8672 (mp) cc_final: 0.8137 (mp) REVERT: C 266 TYR cc_start: 0.7163 (m-80) cc_final: 0.6545 (m-80) REVERT: C 269 TYR cc_start: 0.6169 (m-80) cc_final: 0.5822 (m-80) REVERT: C 347 PHE cc_start: 0.7483 (m-80) cc_final: 0.6077 (m-10) REVERT: C 354 ASN cc_start: 0.8394 (t0) cc_final: 0.7819 (t0) REVERT: C 357 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8071 (ttp80) REVERT: C 414 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8237 (tp-100) REVERT: C 466 ARG cc_start: 0.7960 (ttm110) cc_final: 0.6652 (ptp-170) REVERT: C 473 TYR cc_start: 0.8015 (t80) cc_final: 0.7761 (t80) REVERT: C 490 PHE cc_start: 0.9040 (t80) cc_final: 0.8613 (t80) REVERT: C 1101 HIS cc_start: 0.8294 (m90) cc_final: 0.7828 (m-70) REVERT: H 29 PHE cc_start: 0.8781 (t80) cc_final: 0.8515 (t80) REVERT: H 36 TRP cc_start: 0.6333 (m100) cc_final: 0.5367 (m100) REVERT: H 48 ILE cc_start: 0.8402 (mt) cc_final: 0.8159 (mp) REVERT: H 186 TYR cc_start: 0.8719 (m-80) cc_final: 0.8254 (m-80) REVERT: L 4 MET cc_start: 0.4714 (mtp) cc_final: 0.4056 (mtp) REVERT: L 55 ARG cc_start: 0.9124 (mtm-85) cc_final: 0.8338 (ttm-80) REVERT: L 63 PHE cc_start: 0.8846 (m-80) cc_final: 0.7697 (m-80) REVERT: L 72 PHE cc_start: 0.8983 (m-80) cc_final: 0.8576 (t80) REVERT: L 188 GLU cc_start: 0.7966 (mm-30) cc_final: 0.6893 (pp20) outliers start: 61 outliers final: 32 residues processed: 358 average time/residue: 0.1927 time to fit residues: 109.4464 Evaluate side-chains 327 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 139 optimal weight: 40.0000 chunk 122 optimal weight: 0.0980 chunk 279 optimal weight: 0.8980 chunk 280 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 340 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 787 GLN A 907 ASN A1135 ASN C 317 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1005 GLN H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.170170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101732 restraints weight = 52841.931| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.48 r_work: 0.3138 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28432 Z= 0.127 Angle : 0.568 9.789 38819 Z= 0.292 Chirality : 0.044 0.211 4578 Planarity : 0.004 0.046 4899 Dihedral : 5.153 57.193 5002 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 1.69 % Allowed : 10.39 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3398 helix: 1.39 (0.21), residues: 675 sheet: 0.58 (0.17), residues: 908 loop : -0.39 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 109 TYR 0.034 0.001 TYR A 904 PHE 0.029 0.001 PHE L 119 TRP 0.037 0.002 TRP A 436 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00292 (28325) covalent geometry : angle 0.55667 (38542) SS BOND : bond 0.00288 ( 44) SS BOND : angle 1.64823 ( 88) hydrogen bonds : bond 0.03702 ( 1120) hydrogen bonds : angle 5.64151 ( 3204) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.01541 ( 45) link_BETA1-6 : bond 0.00475 ( 1) link_BETA1-6 : angle 1.34636 ( 3) link_NAG-ASN : bond 0.00240 ( 47) link_NAG-ASN : angle 1.38080 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7804 (m-10) cc_final: 0.7529 (m-10) REVERT: A 104 TRP cc_start: 0.7801 (m-90) cc_final: 0.7436 (m-90) REVERT: A 192 PHE cc_start: 0.8640 (m-80) cc_final: 0.8383 (m-80) REVERT: A 202 LYS cc_start: 0.9111 (mttm) cc_final: 0.8774 (mtpm) REVERT: A 270 LEU cc_start: 0.8746 (mt) cc_final: 0.8135 (mp) REVERT: A 271 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8281 (mm110) REVERT: A 342 PHE cc_start: 0.9360 (m-80) cc_final: 0.9051 (m-80) REVERT: A 354 ASN cc_start: 0.9390 (t0) cc_final: 0.9130 (t0) REVERT: A 392 PHE cc_start: 0.7549 (m-80) cc_final: 0.7230 (m-80) REVERT: A 508 TYR cc_start: 0.8435 (m-80) cc_final: 0.8161 (m-80) REVERT: A 511 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8962 (p) REVERT: A 745 ASP cc_start: 0.7444 (m-30) cc_final: 0.6433 (t0) REVERT: A 979 ASP cc_start: 0.8043 (m-30) cc_final: 0.7832 (t0) REVERT: A 984 LEU cc_start: 0.8815 (mt) cc_final: 0.7878 (tp) REVERT: A 995 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8356 (ttm110) REVERT: B 41 LYS cc_start: 0.8212 (mttp) cc_final: 0.7903 (mtpt) REVERT: B 88 ASP cc_start: 0.8724 (m-30) cc_final: 0.8455 (p0) REVERT: B 231 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8962 (tt) REVERT: B 985 ASP cc_start: 0.8214 (p0) cc_final: 0.7651 (p0) REVERT: C 49 HIS cc_start: 0.7942 (t70) cc_final: 0.7632 (t-170) REVERT: C 86 PHE cc_start: 0.8142 (t80) cc_final: 0.7631 (t80) REVERT: C 104 TRP cc_start: 0.6575 (m-90) cc_final: 0.5812 (m-90) REVERT: C 194 PHE cc_start: 0.8635 (m-10) cc_final: 0.8367 (m-10) REVERT: C 223 LEU cc_start: 0.8571 (mp) cc_final: 0.8116 (mp) REVERT: C 266 TYR cc_start: 0.7054 (m-80) cc_final: 0.6486 (m-80) REVERT: C 269 TYR cc_start: 0.6173 (m-80) cc_final: 0.5869 (m-80) REVERT: C 314 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8090 (tp40) REVERT: C 347 PHE cc_start: 0.7530 (m-80) cc_final: 0.6313 (m-10) REVERT: C 354 ASN cc_start: 0.8499 (t0) cc_final: 0.8099 (t0) REVERT: C 369 TYR cc_start: 0.8181 (t80) cc_final: 0.7557 (t80) REVERT: C 414 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8178 (tp-100) REVERT: C 456 PHE cc_start: 0.8593 (m-10) cc_final: 0.8290 (m-10) REVERT: C 466 ARG cc_start: 0.7910 (ttm110) cc_final: 0.6349 (ptp-170) REVERT: C 473 TYR cc_start: 0.8032 (t80) cc_final: 0.7675 (t80) REVERT: C 490 PHE cc_start: 0.8944 (t80) cc_final: 0.8576 (t80) REVERT: C 1101 HIS cc_start: 0.8106 (m90) cc_final: 0.7775 (m-70) REVERT: H 29 PHE cc_start: 0.8870 (t80) cc_final: 0.8557 (t80) REVERT: H 36 TRP cc_start: 0.6141 (m100) cc_final: 0.5460 (m100) REVERT: H 48 ILE cc_start: 0.8339 (mt) cc_final: 0.8105 (mp) REVERT: H 74 MET cc_start: 0.8561 (mpp) cc_final: 0.7721 (mpp) REVERT: H 186 TYR cc_start: 0.8782 (m-80) cc_final: 0.8303 (m-80) REVERT: L 4 MET cc_start: 0.4665 (mtp) cc_final: 0.3988 (mtp) REVERT: L 55 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8383 (ttm-80) REVERT: L 63 PHE cc_start: 0.8921 (m-80) cc_final: 0.7737 (m-80) REVERT: L 72 PHE cc_start: 0.8882 (m-80) cc_final: 0.8677 (t80) REVERT: L 92 TYR cc_start: 0.8692 (p90) cc_final: 0.7888 (p90) REVERT: L 188 GLU cc_start: 0.7988 (mm-30) cc_final: 0.6958 (pp20) outliers start: 51 outliers final: 33 residues processed: 353 average time/residue: 0.1933 time to fit residues: 108.6893 Evaluate side-chains 316 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 109 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 260 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 312 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 901 GLN A 907 ASN A 935 GLN B 613 GLN B 762 GLN C 125 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103765 restraints weight = 52709.790| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.81 r_work: 0.3126 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28432 Z= 0.164 Angle : 0.566 9.248 38819 Z= 0.291 Chirality : 0.044 0.204 4578 Planarity : 0.004 0.047 4899 Dihedral : 4.895 55.341 5002 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 1.83 % Allowed : 11.35 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3398 helix: 1.34 (0.21), residues: 677 sheet: 0.58 (0.17), residues: 928 loop : -0.40 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.030 0.001 TYR A 904 PHE 0.029 0.001 PHE B 92 TRP 0.037 0.002 TRP A 436 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00383 (28325) covalent geometry : angle 0.55627 (38542) SS BOND : bond 0.00467 ( 44) SS BOND : angle 1.51456 ( 88) hydrogen bonds : bond 0.03710 ( 1120) hydrogen bonds : angle 5.59849 ( 3204) link_BETA1-4 : bond 0.00329 ( 15) link_BETA1-4 : angle 1.05150 ( 45) link_BETA1-6 : bond 0.00435 ( 1) link_BETA1-6 : angle 1.34082 ( 3) link_NAG-ASN : bond 0.00207 ( 47) link_NAG-ASN : angle 1.36572 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7819 (m-10) cc_final: 0.7506 (m-10) REVERT: A 192 PHE cc_start: 0.8645 (m-80) cc_final: 0.8269 (m-80) REVERT: A 202 LYS cc_start: 0.9122 (mttm) cc_final: 0.8825 (mttm) REVERT: A 270 LEU cc_start: 0.8771 (mt) cc_final: 0.8130 (mp) REVERT: A 271 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8296 (mm-40) REVERT: A 342 PHE cc_start: 0.9343 (m-80) cc_final: 0.9068 (m-80) REVERT: A 354 ASN cc_start: 0.9420 (t0) cc_final: 0.9151 (t0) REVERT: A 508 TYR cc_start: 0.8460 (m-80) cc_final: 0.8228 (m-80) REVERT: A 979 ASP cc_start: 0.8083 (m-30) cc_final: 0.7712 (t0) REVERT: A 984 LEU cc_start: 0.8815 (mt) cc_final: 0.7846 (tp) REVERT: A 995 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8278 (ttm110) REVERT: B 41 LYS cc_start: 0.8256 (mttp) cc_final: 0.7683 (mtpt) REVERT: B 88 ASP cc_start: 0.8693 (m-30) cc_final: 0.8478 (p0) REVERT: B 231 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8969 (tt) REVERT: B 988 GLU cc_start: 0.8273 (mp0) cc_final: 0.8056 (mp0) REVERT: C 49 HIS cc_start: 0.7955 (t70) cc_final: 0.7696 (t-170) REVERT: C 86 PHE cc_start: 0.8208 (t80) cc_final: 0.7712 (t80) REVERT: C 104 TRP cc_start: 0.6408 (m-90) cc_final: 0.5884 (m-90) REVERT: C 223 LEU cc_start: 0.8570 (mp) cc_final: 0.8091 (mp) REVERT: C 266 TYR cc_start: 0.6992 (m-80) cc_final: 0.6554 (m-80) REVERT: C 269 TYR cc_start: 0.6259 (m-80) cc_final: 0.5998 (m-80) REVERT: C 314 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8131 (tp40) REVERT: C 347 PHE cc_start: 0.7480 (m-80) cc_final: 0.6330 (m-10) REVERT: C 354 ASN cc_start: 0.8510 (t0) cc_final: 0.8095 (t0) REVERT: C 357 ARG cc_start: 0.8817 (ttp80) cc_final: 0.8069 (ttp80) REVERT: C 364 ASP cc_start: 0.8972 (t0) cc_final: 0.8566 (p0) REVERT: C 414 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8161 (tp-100) REVERT: C 452 LEU cc_start: 0.9323 (mm) cc_final: 0.8804 (tp) REVERT: C 454 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7599 (mtt-85) REVERT: C 456 PHE cc_start: 0.8583 (m-80) cc_final: 0.8319 (m-10) REVERT: C 466 ARG cc_start: 0.7883 (ttm110) cc_final: 0.6171 (ptp-170) REVERT: C 473 TYR cc_start: 0.8034 (t80) cc_final: 0.7660 (t80) REVERT: C 486 PHE cc_start: 0.8196 (t80) cc_final: 0.7018 (t80) REVERT: C 490 PHE cc_start: 0.8941 (t80) cc_final: 0.8537 (t80) REVERT: C 990 GLU cc_start: 0.8262 (pp20) cc_final: 0.7768 (pp20) REVERT: C 994 ASP cc_start: 0.7853 (m-30) cc_final: 0.7622 (m-30) REVERT: C 1101 HIS cc_start: 0.8070 (m90) cc_final: 0.7764 (m-70) REVERT: H 36 TRP cc_start: 0.6074 (m100) cc_final: 0.5254 (m100) REVERT: H 48 ILE cc_start: 0.8366 (mt) cc_final: 0.8115 (mp) REVERT: H 108 ASP cc_start: 0.8620 (p0) cc_final: 0.8330 (p0) REVERT: H 186 TYR cc_start: 0.8862 (m-80) cc_final: 0.8372 (m-80) REVERT: L 4 MET cc_start: 0.4934 (mtp) cc_final: 0.4231 (mtp) REVERT: L 50 TYR cc_start: 0.9087 (p90) cc_final: 0.8667 (p90) REVERT: L 55 ARG cc_start: 0.9169 (mtm-85) cc_final: 0.8110 (ttm-80) REVERT: L 63 PHE cc_start: 0.8948 (m-80) cc_final: 0.7814 (m-80) REVERT: L 72 PHE cc_start: 0.8840 (m-80) cc_final: 0.8428 (t80) REVERT: L 78 ARG cc_start: 0.9569 (mmp80) cc_final: 0.9350 (mmp80) REVERT: L 141 TYR cc_start: 0.7966 (t80) cc_final: 0.7765 (t80) REVERT: L 188 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7162 (pp20) outliers start: 55 outliers final: 38 residues processed: 341 average time/residue: 0.1883 time to fit residues: 103.2988 Evaluate side-chains 312 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 110 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 278 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 320 optimal weight: 30.0000 chunk 263 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 613 GLN B 762 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.169685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099828 restraints weight = 52764.423| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.19 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28432 Z= 0.137 Angle : 0.558 13.365 38819 Z= 0.285 Chirality : 0.044 0.200 4578 Planarity : 0.004 0.048 4899 Dihedral : 4.677 52.020 5002 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 11.85 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3398 helix: 1.40 (0.21), residues: 680 sheet: 0.55 (0.17), residues: 933 loop : -0.40 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.026 0.001 TYR L 92 PHE 0.028 0.001 PHE B 92 TRP 0.040 0.002 TRP A 436 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00316 (28325) covalent geometry : angle 0.54994 (38542) SS BOND : bond 0.00231 ( 44) SS BOND : angle 1.20739 ( 88) hydrogen bonds : bond 0.03591 ( 1120) hydrogen bonds : angle 5.49649 ( 3204) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.01640 ( 45) link_BETA1-6 : bond 0.00431 ( 1) link_BETA1-6 : angle 1.32782 ( 3) link_NAG-ASN : bond 0.00193 ( 47) link_NAG-ASN : angle 1.28864 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 296 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7810 (m-10) cc_final: 0.7594 (m-10) REVERT: A 192 PHE cc_start: 0.8650 (m-80) cc_final: 0.8234 (m-80) REVERT: A 201 PHE cc_start: 0.8579 (t80) cc_final: 0.8299 (t80) REVERT: A 270 LEU cc_start: 0.8774 (mt) cc_final: 0.8109 (mp) REVERT: A 271 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8307 (mm-40) REVERT: A 342 PHE cc_start: 0.9350 (m-80) cc_final: 0.9072 (m-80) REVERT: A 354 ASN cc_start: 0.9410 (t0) cc_final: 0.9148 (t0) REVERT: A 508 TYR cc_start: 0.8416 (m-80) cc_final: 0.8178 (m-80) REVERT: A 745 ASP cc_start: 0.7206 (m-30) cc_final: 0.6277 (t0) REVERT: A 755 GLN cc_start: 0.8540 (mt0) cc_final: 0.8327 (mt0) REVERT: A 976 VAL cc_start: 0.8911 (t) cc_final: 0.8683 (m) REVERT: A 979 ASP cc_start: 0.8110 (m-30) cc_final: 0.7750 (t0) REVERT: A 984 LEU cc_start: 0.8821 (mt) cc_final: 0.7845 (tp) REVERT: A 995 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8318 (ttm110) REVERT: B 41 LYS cc_start: 0.8241 (mttp) cc_final: 0.7758 (mtpt) REVERT: B 231 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8959 (tt) REVERT: B 387 LEU cc_start: 0.8570 (mt) cc_final: 0.8300 (mt) REVERT: C 49 HIS cc_start: 0.7926 (t70) cc_final: 0.7674 (t70) REVERT: C 86 PHE cc_start: 0.8202 (t80) cc_final: 0.7698 (t80) REVERT: C 104 TRP cc_start: 0.6394 (m-90) cc_final: 0.5849 (m-90) REVERT: C 223 LEU cc_start: 0.8480 (mp) cc_final: 0.8005 (mp) REVERT: C 266 TYR cc_start: 0.6933 (m-80) cc_final: 0.6568 (m-80) REVERT: C 269 TYR cc_start: 0.6250 (m-80) cc_final: 0.6011 (m-80) REVERT: C 347 PHE cc_start: 0.7552 (m-80) cc_final: 0.6487 (m-10) REVERT: C 354 ASN cc_start: 0.8493 (t0) cc_final: 0.8060 (t0) REVERT: C 357 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8091 (ttp80) REVERT: C 369 TYR cc_start: 0.7925 (t80) cc_final: 0.7647 (t80) REVERT: C 414 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8160 (tp-100) REVERT: C 454 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7182 (mtt180) REVERT: C 456 PHE cc_start: 0.8599 (m-80) cc_final: 0.8233 (m-80) REVERT: C 466 ARG cc_start: 0.7912 (ttm110) cc_final: 0.6238 (ptp-170) REVERT: C 473 TYR cc_start: 0.8044 (t80) cc_final: 0.7694 (t80) REVERT: C 486 PHE cc_start: 0.7694 (t80) cc_final: 0.7041 (t80) REVERT: C 490 PHE cc_start: 0.8934 (t80) cc_final: 0.8503 (t80) REVERT: C 1101 HIS cc_start: 0.8064 (m90) cc_final: 0.7736 (m-70) REVERT: H 36 TRP cc_start: 0.6093 (m100) cc_final: 0.5331 (m100) REVERT: H 48 ILE cc_start: 0.8388 (mt) cc_final: 0.8157 (mp) REVERT: H 74 MET cc_start: 0.8480 (mpp) cc_final: 0.8258 (mpp) REVERT: H 108 ASP cc_start: 0.8631 (p0) cc_final: 0.8384 (p0) REVERT: H 186 TYR cc_start: 0.8851 (m-80) cc_final: 0.8334 (m-80) REVERT: L 4 MET cc_start: 0.5128 (mtp) cc_final: 0.2429 (mmm) REVERT: L 50 TYR cc_start: 0.8942 (p90) cc_final: 0.8468 (p90) REVERT: L 55 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8230 (ttm-80) REVERT: L 63 PHE cc_start: 0.8994 (m-80) cc_final: 0.7821 (m-80) REVERT: L 72 PHE cc_start: 0.8756 (m-80) cc_final: 0.8416 (t80) REVERT: L 92 TYR cc_start: 0.8328 (p90) cc_final: 0.7047 (p90) REVERT: L 141 TYR cc_start: 0.7843 (t80) cc_final: 0.7606 (t80) REVERT: L 188 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7209 (pp20) outliers start: 58 outliers final: 46 residues processed: 338 average time/residue: 0.1764 time to fit residues: 96.5319 Evaluate side-chains 323 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 300 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 338 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 291 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 762 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 853 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.169722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105337 restraints weight = 52713.813| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.25 r_work: 0.3106 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 28432 Z= 0.148 Angle : 0.567 11.169 38819 Z= 0.290 Chirality : 0.044 0.198 4578 Planarity : 0.004 0.046 4899 Dihedral : 4.562 51.981 5002 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.76 % Allowed : 12.55 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3398 helix: 1.45 (0.20), residues: 671 sheet: 0.56 (0.17), residues: 932 loop : -0.41 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 38 TYR 0.021 0.001 TYR L 92 PHE 0.028 0.001 PHE B 92 TRP 0.044 0.002 TRP A 436 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00344 (28325) covalent geometry : angle 0.55638 (38542) SS BOND : bond 0.00315 ( 44) SS BOND : angle 1.73393 ( 88) hydrogen bonds : bond 0.03623 ( 1120) hydrogen bonds : angle 5.46713 ( 3204) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.01748 ( 45) link_BETA1-6 : bond 0.00357 ( 1) link_BETA1-6 : angle 1.26233 ( 3) link_NAG-ASN : bond 0.00183 ( 47) link_NAG-ASN : angle 1.28764 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7819 (m-10) cc_final: 0.7590 (m-10) REVERT: A 192 PHE cc_start: 0.8642 (m-80) cc_final: 0.8261 (m-80) REVERT: A 270 LEU cc_start: 0.8774 (mt) cc_final: 0.8075 (mp) REVERT: A 271 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8320 (mm-40) REVERT: A 342 PHE cc_start: 0.9333 (m-80) cc_final: 0.9078 (m-80) REVERT: A 354 ASN cc_start: 0.9409 (t0) cc_final: 0.9143 (t0) REVERT: A 508 TYR cc_start: 0.8411 (m-80) cc_final: 0.8175 (m-80) REVERT: A 779 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8505 (tp40) REVERT: A 976 VAL cc_start: 0.8908 (t) cc_final: 0.8663 (m) REVERT: A 979 ASP cc_start: 0.8094 (m-30) cc_final: 0.7754 (t0) REVERT: A 995 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8341 (ttm110) REVERT: B 41 LYS cc_start: 0.8231 (mttp) cc_final: 0.7573 (mtpt) REVERT: B 231 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8961 (tt) REVERT: B 387 LEU cc_start: 0.8596 (mt) cc_final: 0.8321 (mt) REVERT: C 49 HIS cc_start: 0.7945 (t70) cc_final: 0.7554 (t-90) REVERT: C 86 PHE cc_start: 0.8232 (t80) cc_final: 0.7702 (t80) REVERT: C 104 TRP cc_start: 0.6368 (m-90) cc_final: 0.5842 (m-90) REVERT: C 266 TYR cc_start: 0.6928 (m-80) cc_final: 0.6621 (m-80) REVERT: C 269 TYR cc_start: 0.6358 (m-80) cc_final: 0.6087 (m-80) REVERT: C 347 PHE cc_start: 0.7569 (m-80) cc_final: 0.6569 (m-10) REVERT: C 354 ASN cc_start: 0.8506 (t0) cc_final: 0.8061 (t0) REVERT: C 357 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8087 (ttp80) REVERT: C 369 TYR cc_start: 0.8015 (t80) cc_final: 0.7629 (t80) REVERT: C 414 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8203 (tp-100) REVERT: C 452 LEU cc_start: 0.9296 (mm) cc_final: 0.8751 (tp) REVERT: C 454 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7223 (mtt180) REVERT: C 456 PHE cc_start: 0.8610 (m-80) cc_final: 0.8288 (m-80) REVERT: C 466 ARG cc_start: 0.7868 (ttm110) cc_final: 0.6182 (ptp-170) REVERT: C 473 TYR cc_start: 0.8052 (t80) cc_final: 0.7698 (t80) REVERT: C 486 PHE cc_start: 0.7748 (t80) cc_final: 0.7426 (t80) REVERT: C 490 PHE cc_start: 0.8935 (t80) cc_final: 0.8478 (t80) REVERT: C 1101 HIS cc_start: 0.8097 (m90) cc_final: 0.7766 (m-70) REVERT: H 36 TRP cc_start: 0.6117 (m100) cc_final: 0.5348 (m100) REVERT: H 48 ILE cc_start: 0.8397 (mt) cc_final: 0.8169 (mp) REVERT: H 74 MET cc_start: 0.8569 (mpp) cc_final: 0.8080 (mmm) REVERT: H 186 TYR cc_start: 0.8854 (m-80) cc_final: 0.8357 (m-80) REVERT: L 4 MET cc_start: 0.5134 (mtp) cc_final: 0.2524 (mmm) REVERT: L 50 TYR cc_start: 0.8873 (p90) cc_final: 0.8447 (p90) REVERT: L 55 ARG cc_start: 0.9155 (mtm-85) cc_final: 0.8187 (ttm-80) REVERT: L 63 PHE cc_start: 0.9036 (m-80) cc_final: 0.7793 (m-80) REVERT: L 72 PHE cc_start: 0.8781 (m-80) cc_final: 0.8402 (t80) REVERT: L 78 ARG cc_start: 0.9543 (mmp80) cc_final: 0.9056 (mmp80) REVERT: L 82 GLU cc_start: 0.9243 (pm20) cc_final: 0.8865 (pm20) REVERT: L 92 TYR cc_start: 0.8285 (p90) cc_final: 0.7636 (p90) REVERT: L 141 TYR cc_start: 0.8076 (t80) cc_final: 0.7769 (t80) REVERT: L 188 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7324 (pp20) outliers start: 53 outliers final: 41 residues processed: 331 average time/residue: 0.1839 time to fit residues: 97.8521 Evaluate side-chains 318 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 320 optimal weight: 30.0000 chunk 256 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.169639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.103871 restraints weight = 52807.052| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.60 r_work: 0.3114 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28432 Z= 0.135 Angle : 0.563 10.826 38819 Z= 0.287 Chirality : 0.044 0.204 4578 Planarity : 0.004 0.061 4899 Dihedral : 4.442 52.096 5002 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.73 % Allowed : 12.98 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3398 helix: 1.54 (0.20), residues: 668 sheet: 0.52 (0.17), residues: 944 loop : -0.40 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 87 TYR 0.028 0.001 TYR A 451 PHE 0.033 0.001 PHE L 119 TRP 0.049 0.002 TRP A 436 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00314 (28325) covalent geometry : angle 0.55421 (38542) SS BOND : bond 0.00247 ( 44) SS BOND : angle 1.48060 ( 88) hydrogen bonds : bond 0.03567 ( 1120) hydrogen bonds : angle 5.42227 ( 3204) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.00618 ( 45) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.27705 ( 3) link_NAG-ASN : bond 0.00181 ( 47) link_NAG-ASN : angle 1.24397 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 288 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7853 (m-10) cc_final: 0.7593 (m-10) REVERT: A 104 TRP cc_start: 0.7896 (m-90) cc_final: 0.7500 (m-90) REVERT: A 192 PHE cc_start: 0.8646 (m-80) cc_final: 0.8397 (m-80) REVERT: A 270 LEU cc_start: 0.8798 (mt) cc_final: 0.8092 (mp) REVERT: A 271 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8322 (mm-40) REVERT: A 342 PHE cc_start: 0.9366 (m-80) cc_final: 0.9104 (m-80) REVERT: A 354 ASN cc_start: 0.9401 (t0) cc_final: 0.9137 (t0) REVERT: A 495 TYR cc_start: 0.7278 (m-80) cc_final: 0.6601 (m-80) REVERT: A 508 TYR cc_start: 0.8418 (m-80) cc_final: 0.8180 (m-80) REVERT: A 745 ASP cc_start: 0.7295 (m-30) cc_final: 0.6321 (t0) REVERT: A 779 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8509 (tp40) REVERT: A 976 VAL cc_start: 0.8928 (t) cc_final: 0.8664 (m) REVERT: A 979 ASP cc_start: 0.8134 (m-30) cc_final: 0.7767 (t0) REVERT: A 984 LEU cc_start: 0.8773 (mt) cc_final: 0.7795 (tp) REVERT: B 41 LYS cc_start: 0.8208 (mttp) cc_final: 0.7759 (mtpt) REVERT: B 231 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8946 (tt) REVERT: B 387 LEU cc_start: 0.8598 (mt) cc_final: 0.8329 (mt) REVERT: C 49 HIS cc_start: 0.7950 (t70) cc_final: 0.7576 (t-90) REVERT: C 86 PHE cc_start: 0.8273 (t80) cc_final: 0.7747 (t80) REVERT: C 104 TRP cc_start: 0.6391 (m-90) cc_final: 0.5861 (m-90) REVERT: C 223 LEU cc_start: 0.8315 (mp) cc_final: 0.7382 (mp) REVERT: C 266 TYR cc_start: 0.6895 (m-80) cc_final: 0.6634 (m-80) REVERT: C 269 TYR cc_start: 0.6347 (m-80) cc_final: 0.6082 (m-80) REVERT: C 329 PHE cc_start: 0.8479 (m-10) cc_final: 0.8148 (m-80) REVERT: C 354 ASN cc_start: 0.8473 (t0) cc_final: 0.7853 (t0) REVERT: C 357 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8511 (ttp80) REVERT: C 369 TYR cc_start: 0.8093 (t80) cc_final: 0.7625 (t80) REVERT: C 414 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8216 (tp-100) REVERT: C 452 LEU cc_start: 0.9297 (mm) cc_final: 0.8747 (tp) REVERT: C 454 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7616 (mtt-85) REVERT: C 456 PHE cc_start: 0.8602 (m-80) cc_final: 0.8384 (m-80) REVERT: C 466 ARG cc_start: 0.7902 (ttm110) cc_final: 0.6201 (ptp-170) REVERT: C 473 TYR cc_start: 0.8030 (t80) cc_final: 0.7710 (t80) REVERT: C 486 PHE cc_start: 0.7793 (t80) cc_final: 0.7423 (t80) REVERT: C 490 PHE cc_start: 0.8944 (t80) cc_final: 0.8489 (t80) REVERT: C 990 GLU cc_start: 0.8327 (pp20) cc_final: 0.7705 (pp20) REVERT: C 994 ASP cc_start: 0.7963 (m-30) cc_final: 0.7701 (m-30) REVERT: C 1101 HIS cc_start: 0.8133 (m90) cc_final: 0.7803 (m-70) REVERT: H 36 TRP cc_start: 0.6058 (m100) cc_final: 0.5613 (m100) REVERT: H 74 MET cc_start: 0.8539 (mpp) cc_final: 0.8077 (mmm) REVERT: H 108 ASP cc_start: 0.8719 (p0) cc_final: 0.8508 (p0) REVERT: H 186 TYR cc_start: 0.8859 (m-80) cc_final: 0.8350 (m-80) REVERT: L 4 MET cc_start: 0.5047 (mtp) cc_final: 0.2421 (mmm) REVERT: L 50 TYR cc_start: 0.8871 (p90) cc_final: 0.8425 (p90) REVERT: L 55 ARG cc_start: 0.9123 (mtm-85) cc_final: 0.8172 (ttm-80) REVERT: L 63 PHE cc_start: 0.9015 (m-80) cc_final: 0.7810 (m-80) REVERT: L 72 PHE cc_start: 0.8777 (m-80) cc_final: 0.8401 (t80) REVERT: L 92 TYR cc_start: 0.8343 (p90) cc_final: 0.7638 (p90) REVERT: L 141 TYR cc_start: 0.8059 (t80) cc_final: 0.7713 (t80) REVERT: L 188 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7356 (pp20) outliers start: 52 outliers final: 43 residues processed: 331 average time/residue: 0.1786 time to fit residues: 95.8568 Evaluate side-chains 326 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 297 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 48 optimal weight: 0.0030 chunk 107 optimal weight: 0.0980 chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 913 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** H 3 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 = 0.4381 r_free = 0.4381 target = 0.170560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102065 restraints weight = 52806.328| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.15 r_work: 0.3185 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28432 Z= 0.107 Angle : 0.557 10.294 38819 Z= 0.285 Chirality : 0.044 0.200 4578 Planarity : 0.004 0.055 4899 Dihedral : 4.261 52.489 5002 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.59 % Allowed : 13.21 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3398 helix: 1.73 (0.21), residues: 664 sheet: 0.55 (0.17), residues: 943 loop : -0.39 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 78 TYR 0.037 0.001 TYR A 451 PHE 0.025 0.001 PHE B 92 TRP 0.055 0.002 TRP A 436 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00243 (28325) covalent geometry : angle 0.54919 (38542) SS BOND : bond 0.00213 ( 44) SS BOND : angle 1.36275 ( 88) hydrogen bonds : bond 0.03397 ( 1120) hydrogen bonds : angle 5.30101 ( 3204) link_BETA1-4 : bond 0.00382 ( 15) link_BETA1-4 : angle 0.98165 ( 45) link_BETA1-6 : bond 0.00447 ( 1) link_BETA1-6 : angle 1.21983 ( 3) link_NAG-ASN : bond 0.00197 ( 47) link_NAG-ASN : angle 1.17711 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7749 (m-10) cc_final: 0.7447 (m-10) REVERT: A 84 LEU cc_start: 0.9025 (mm) cc_final: 0.8729 (tp) REVERT: A 104 TRP cc_start: 0.7826 (m-90) cc_final: 0.7455 (m-90) REVERT: A 192 PHE cc_start: 0.8634 (m-80) cc_final: 0.8395 (m-80) REVERT: A 202 LYS cc_start: 0.9104 (mttm) cc_final: 0.8819 (mttm) REVERT: A 270 LEU cc_start: 0.8773 (mt) cc_final: 0.8090 (mp) REVERT: A 271 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8325 (mm-40) REVERT: A 354 ASN cc_start: 0.9410 (t0) cc_final: 0.9163 (t0) REVERT: A 495 TYR cc_start: 0.7107 (m-80) cc_final: 0.6422 (m-80) REVERT: A 505 TYR cc_start: 0.8335 (t80) cc_final: 0.8057 (t80) REVERT: A 508 TYR cc_start: 0.8391 (m-80) cc_final: 0.8176 (m-80) REVERT: A 745 ASP cc_start: 0.7269 (m-30) cc_final: 0.6304 (t0) REVERT: A 779 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8488 (tp40) REVERT: A 976 VAL cc_start: 0.8888 (t) cc_final: 0.8632 (m) REVERT: A 979 ASP cc_start: 0.8104 (m-30) cc_final: 0.7744 (t0) REVERT: A 984 LEU cc_start: 0.8763 (mt) cc_final: 0.7778 (tp) REVERT: A 990 GLU cc_start: 0.7897 (tp30) cc_final: 0.7297 (tp30) REVERT: B 41 LYS cc_start: 0.8202 (mttp) cc_final: 0.7611 (mtpt) REVERT: B 231 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8910 (tt) REVERT: B 387 LEU cc_start: 0.8553 (mt) cc_final: 0.8307 (mt) REVERT: C 49 HIS cc_start: 0.7915 (t70) cc_final: 0.7528 (t-90) REVERT: C 86 PHE cc_start: 0.8206 (t80) cc_final: 0.7642 (t80) REVERT: C 223 LEU cc_start: 0.8330 (mp) cc_final: 0.7387 (mp) REVERT: C 329 PHE cc_start: 0.8425 (m-10) cc_final: 0.8174 (m-10) REVERT: C 347 PHE cc_start: 0.7409 (m-80) cc_final: 0.5819 (m-80) REVERT: C 354 ASN cc_start: 0.8382 (t0) cc_final: 0.7771 (t0) REVERT: C 357 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8526 (ttp80) REVERT: C 369 TYR cc_start: 0.8080 (t80) cc_final: 0.7599 (t80) REVERT: C 414 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8274 (tp-100) REVERT: C 452 LEU cc_start: 0.9311 (mm) cc_final: 0.8730 (tp) REVERT: C 454 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7077 (mtt180) REVERT: C 466 ARG cc_start: 0.7969 (ttm110) cc_final: 0.6343 (ptp-170) REVERT: C 473 TYR cc_start: 0.8044 (t80) cc_final: 0.7714 (t80) REVERT: C 486 PHE cc_start: 0.7889 (t80) cc_final: 0.7143 (t80) REVERT: C 490 PHE cc_start: 0.8949 (t80) cc_final: 0.8520 (t80) REVERT: C 492 LEU cc_start: 0.9649 (mt) cc_final: 0.9386 (mp) REVERT: C 1101 HIS cc_start: 0.8005 (m90) cc_final: 0.7680 (m-70) REVERT: H 36 TRP cc_start: 0.5802 (m100) cc_final: 0.5340 (m100) REVERT: H 74 MET cc_start: 0.8524 (mpp) cc_final: 0.8078 (mmm) REVERT: H 108 ASP cc_start: 0.8713 (p0) cc_final: 0.8366 (p0) REVERT: H 186 TYR cc_start: 0.8869 (m-80) cc_final: 0.8360 (m-80) REVERT: L 4 MET cc_start: 0.5052 (mtp) cc_final: 0.2581 (mmm) REVERT: L 50 TYR cc_start: 0.8781 (p90) cc_final: 0.8356 (p90) REVERT: L 55 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8152 (ttm-80) REVERT: L 63 PHE cc_start: 0.9097 (m-80) cc_final: 0.7924 (m-80) REVERT: L 72 PHE cc_start: 0.8695 (m-80) cc_final: 0.8395 (t80) REVERT: L 92 TYR cc_start: 0.8317 (p90) cc_final: 0.7067 (p90) REVERT: L 141 TYR cc_start: 0.8025 (t80) cc_final: 0.7664 (t80) REVERT: L 188 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7332 (pp20) outliers start: 48 outliers final: 41 residues processed: 341 average time/residue: 0.1787 time to fit residues: 98.6964 Evaluate side-chains 327 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 310 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 306 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 110 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 317 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN B 99 ASN B 317 ASN B 613 GLN B 762 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.167481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.098615 restraints weight = 52615.471| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.51 r_work: 0.3035 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 28432 Z= 0.257 Angle : 0.636 9.453 38819 Z= 0.327 Chirality : 0.046 0.204 4578 Planarity : 0.004 0.050 4899 Dihedral : 4.544 51.547 5002 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.66 % Allowed : 13.68 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3398 helix: 1.35 (0.20), residues: 661 sheet: 0.54 (0.17), residues: 932 loop : -0.50 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 78 TYR 0.031 0.002 TYR A 451 PHE 0.031 0.002 PHE B 92 TRP 0.062 0.002 TRP A 436 HIS 0.010 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00605 (28325) covalent geometry : angle 0.62512 (38542) SS BOND : bond 0.00414 ( 44) SS BOND : angle 1.81947 ( 88) hydrogen bonds : bond 0.04112 ( 1120) hydrogen bonds : angle 5.63676 ( 3204) link_BETA1-4 : bond 0.00210 ( 15) link_BETA1-4 : angle 1.15931 ( 45) link_BETA1-6 : bond 0.00345 ( 1) link_BETA1-6 : angle 1.40336 ( 3) link_NAG-ASN : bond 0.00260 ( 47) link_NAG-ASN : angle 1.41679 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7888 (m-10) cc_final: 0.7581 (m-10) REVERT: A 84 LEU cc_start: 0.9005 (mm) cc_final: 0.8708 (tp) REVERT: A 192 PHE cc_start: 0.8689 (m-80) cc_final: 0.8275 (m-80) REVERT: A 202 LYS cc_start: 0.9128 (mttm) cc_final: 0.8833 (mttm) REVERT: A 270 LEU cc_start: 0.8860 (mt) cc_final: 0.8074 (mp) REVERT: A 271 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8187 (mm110) REVERT: A 342 PHE cc_start: 0.9325 (m-80) cc_final: 0.9034 (m-80) REVERT: A 351 TYR cc_start: 0.8512 (p90) cc_final: 0.7927 (p90) REVERT: A 354 ASN cc_start: 0.9406 (t0) cc_final: 0.9158 (t0) REVERT: A 508 TYR cc_start: 0.8520 (m-80) cc_final: 0.8279 (m-80) REVERT: A 779 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: A 976 VAL cc_start: 0.8937 (t) cc_final: 0.8679 (m) REVERT: A 979 ASP cc_start: 0.8150 (m-30) cc_final: 0.7840 (t0) REVERT: A 984 LEU cc_start: 0.8816 (mt) cc_final: 0.7717 (tp) REVERT: B 41 LYS cc_start: 0.8280 (mttp) cc_final: 0.7772 (mtpt) REVERT: B 231 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8923 (tt) REVERT: B 387 LEU cc_start: 0.8659 (mt) cc_final: 0.8369 (mt) REVERT: B 567 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7973 (tpp80) REVERT: C 49 HIS cc_start: 0.7980 (t70) cc_final: 0.7611 (t-90) REVERT: C 86 PHE cc_start: 0.8312 (t80) cc_final: 0.7498 (t80) REVERT: C 223 LEU cc_start: 0.8414 (mp) cc_final: 0.7442 (mp) REVERT: C 266 TYR cc_start: 0.7149 (m-80) cc_final: 0.5970 (m-10) REVERT: C 329 PHE cc_start: 0.8480 (m-10) cc_final: 0.8212 (m-10) REVERT: C 347 PHE cc_start: 0.7412 (m-80) cc_final: 0.5820 (m-10) REVERT: C 354 ASN cc_start: 0.8500 (t0) cc_final: 0.7907 (t0) REVERT: C 357 ARG cc_start: 0.8788 (ttp80) cc_final: 0.7807 (ttp80) REVERT: C 369 TYR cc_start: 0.8207 (t80) cc_final: 0.7692 (t80) REVERT: C 414 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8297 (tp-100) REVERT: C 452 LEU cc_start: 0.9351 (mm) cc_final: 0.8823 (tp) REVERT: C 466 ARG cc_start: 0.7930 (ttm110) cc_final: 0.6541 (ptp-170) REVERT: C 471 GLU cc_start: 0.8591 (mp0) cc_final: 0.8302 (mp0) REVERT: C 473 TYR cc_start: 0.8128 (t80) cc_final: 0.7784 (t80) REVERT: C 486 PHE cc_start: 0.7840 (t80) cc_final: 0.7118 (t80) REVERT: C 490 PHE cc_start: 0.8987 (t80) cc_final: 0.8530 (t80) REVERT: C 492 LEU cc_start: 0.9689 (mt) cc_final: 0.9442 (mp) REVERT: C 1101 HIS cc_start: 0.8197 (m90) cc_final: 0.7849 (m-70) REVERT: H 36 TRP cc_start: 0.6010 (m100) cc_final: 0.5484 (m100) REVERT: H 74 MET cc_start: 0.8596 (mpp) cc_final: 0.8140 (mmm) REVERT: H 108 ASP cc_start: 0.8761 (p0) cc_final: 0.8517 (p0) REVERT: H 186 TYR cc_start: 0.8898 (m-80) cc_final: 0.8399 (m-80) REVERT: L 4 MET cc_start: 0.5063 (mtp) cc_final: 0.2575 (mmm) REVERT: L 50 TYR cc_start: 0.8751 (p90) cc_final: 0.8487 (p90) REVERT: L 63 PHE cc_start: 0.9157 (m-80) cc_final: 0.8381 (m-80) REVERT: L 72 PHE cc_start: 0.8799 (m-80) cc_final: 0.8380 (t80) REVERT: L 92 TYR cc_start: 0.8517 (p90) cc_final: 0.7270 (p90) REVERT: L 141 TYR cc_start: 0.8073 (t80) cc_final: 0.7709 (t80) REVERT: L 188 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7388 (pp20) outliers start: 50 outliers final: 42 residues processed: 328 average time/residue: 0.1911 time to fit residues: 100.2503 Evaluate side-chains 322 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 243 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 266 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 238 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 292 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 450 ASN B 99 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.168902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102905 restraints weight = 52770.510| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.52 r_work: 0.3099 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28432 Z= 0.155 Angle : 0.589 9.531 38819 Z= 0.302 Chirality : 0.045 0.337 4578 Planarity : 0.004 0.051 4899 Dihedral : 4.437 52.018 5002 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.46 % Allowed : 13.88 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3398 helix: 1.46 (0.20), residues: 667 sheet: 0.51 (0.17), residues: 936 loop : -0.47 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 67 TYR 0.025 0.001 TYR A 451 PHE 0.036 0.001 PHE C 220 TRP 0.062 0.002 TRP A 436 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00364 (28325) covalent geometry : angle 0.58051 (38542) SS BOND : bond 0.00257 ( 44) SS BOND : angle 1.50228 ( 88) hydrogen bonds : bond 0.03683 ( 1120) hydrogen bonds : angle 5.47341 ( 3204) link_BETA1-4 : bond 0.00314 ( 15) link_BETA1-4 : angle 1.01839 ( 45) link_BETA1-6 : bond 0.00415 ( 1) link_BETA1-6 : angle 1.25221 ( 3) link_NAG-ASN : bond 0.00188 ( 47) link_NAG-ASN : angle 1.24102 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9006.83 seconds wall clock time: 154 minutes 34.74 seconds (9274.74 seconds total)