Starting phenix.real_space_refine on Sun Sep 13 14:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.map" model { file = "/net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo5_67070/09_2026/9xo5_67070.cif" } resolution = 3.75 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= 0.002 sd= 0.033 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 111 5.16 5 C 14841 2.51 5 N 3702 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23280 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7531 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 37, 'TRANS': 944} Chain breaks: 16 Chain: "B" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7531 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 37, 'TRANS': 944} Chain breaks: 16 Chain: "C" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7531 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 37, 'TRANS': 944} Chain breaks: 16 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.62, per 1000 atoms: 0.24 Number of scatterers: 23280 At special positions: 0 Unit cell: (138.6, 142.56, 158.4, 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 111 16.00 O 4626 8.00 N 3702 7.00 C 14841 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.03 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA I 3 " - " MAN I 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA I 3 " - " MAN I 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1401 " - " ASN A 216 " " NAG A1402 " - " ASN A 344 " " NAG A1403 " - " ASN A 726 " " NAG A1404 " - " ASN A 781 " " NAG A1405 " - " ASN A 514 " " NAG A1406 " - " ASN A 743 " " NAG A1407 " - " ASN A 787 " " NAG A1408 " - " ASN A 873 " " NAG B1401 " - " ASN B 216 " " NAG B1402 " - " ASN B 344 " " NAG B1403 " - " ASN B 726 " " NAG B1404 " - " ASN B 781 " " NAG B1405 " - " ASN B 514 " " NAG B1406 " - " ASN B 743 " " NAG B1407 " - " ASN B 787 " " NAG B1408 " - " ASN B 873 " " NAG C1401 " - " ASN C 216 " " NAG C1402 " - " ASN C 344 " " NAG C1403 " - " ASN C 726 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C 514 " " NAG C1406 " - " ASN C 743 " " NAG C1407 " - " ASN C 787 " " NAG C1408 " - " ASN C 873 " " NAG D 1 " - " ASN A 324 " " NAG E 1 " - " ASN A 688 " " NAG F 1 " - " ASN A 264 " " NAG G 1 " - " ASN B 324 " " NAG H 1 " - " ASN B 688 " " NAG I 1 " - " ASN B 264 " " NAG J 1 " - " ASN C 324 " " NAG K 1 " - " ASN C 688 " " NAG L 1 " - " ASN C 264 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 43 sheets defined 23.8% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.900A pdb=" N LYS A 38 " --> pdb=" O PHE A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.717A pdb=" N ILE A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 807 through 813 removed outlier: 3.934A pdb=" N TYR A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 4.021A pdb=" N GLN A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.951A pdb=" N LEU A 839 " --> pdb=" O SER A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.531A pdb=" N LEU A 878 " --> pdb=" O THR A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 928 through 936 removed outlier: 3.518A pdb=" N SER A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.836A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1014 Processing helix chain 'A' and resid 1030 through 1045 removed outlier: 3.596A pdb=" N GLN A1045 " --> pdb=" O VAL A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1066 through 1074 removed outlier: 3.770A pdb=" N LEU A1074 " --> pdb=" O ILE A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.786A pdb=" N VAL A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A1084 " --> pdb=" O ASP A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1220 removed outlier: 3.543A pdb=" N PHE A1220 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.953A pdb=" N LYS B 38 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.693A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 476 Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.976A pdb=" N LEU B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 860 removed outlier: 3.700A pdb=" N GLN B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 928 through 936 removed outlier: 3.525A pdb=" N SER B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 959 Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.981A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1014 Processing helix chain 'B' and resid 1030 through 1045 removed outlier: 3.640A pdb=" N GLN B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1055 Processing helix chain 'B' and resid 1066 through 1074 removed outlier: 3.819A pdb=" N LEU B1074 " --> pdb=" O ILE B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1123 removed outlier: 3.524A pdb=" N ALA B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B1084 " --> pdb=" O ASP B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1220 removed outlier: 3.523A pdb=" N PHE B1220 " --> pdb=" O VAL B1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.917A pdb=" N LYS C 38 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 325 through 333 removed outlier: 3.698A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 807 through 813 removed outlier: 3.914A pdb=" N TYR C 811 " --> pdb=" O ASP C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 830 through 852 removed outlier: 4.007A pdb=" N LEU C 839 " --> pdb=" O SER C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 861 removed outlier: 3.577A pdb=" N LEU C 861 " --> pdb=" O GLU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.556A pdb=" N LEU C 878 " --> pdb=" O THR C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 903 Processing helix chain 'C' and resid 928 through 936 removed outlier: 3.508A pdb=" N SER C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 959 Processing helix chain 'C' and resid 973 through 986 removed outlier: 4.176A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 985 " --> pdb=" O ARG C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1013 Processing helix chain 'C' and resid 1030 through 1045 removed outlier: 3.589A pdb=" N GLN C1045 " --> pdb=" O VAL C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1055 Processing helix chain 'C' and resid 1066 through 1074 removed outlier: 3.808A pdb=" N LEU C1074 " --> pdb=" O ILE C1070 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.595A pdb=" N ALA C1079 " --> pdb=" O ASP C1075 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C1084 " --> pdb=" O ASP C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1220 removed outlier: 3.568A pdb=" N PHE C1220 " --> pdb=" O VAL C1217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 48 removed outlier: 3.600A pdb=" N VAL A 47 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 226 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.355A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.355A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.622A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 344 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 348 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA A 389 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 375 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE A 387 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 377 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR A 385 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.151A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 718 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 531 through 536 removed outlier: 4.069A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 550 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 517 " --> pdb=" O PHE A 554 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 5.050A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 616 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 654 removed outlier: 3.592A pdb=" N GLY A 659 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 685 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 798 removed outlier: 3.648A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A1154 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 780 through 798 removed outlier: 3.648A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A1154 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A1189 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB5, first strand: chain 'A' and resid 1171 through 1174 removed outlier: 3.554A pdb=" N ILE A1178 " --> pdb=" O VAL A1174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.901A pdb=" N ALA B 45 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 226 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 79 through 81 Processing sheet with id=AB8, first strand: chain 'B' and resid 270 through 286 removed outlier: 7.253A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 283 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 440 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 286 removed outlier: 7.253A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 283 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 452 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 296 through 298 removed outlier: 4.494A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 348 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B 373 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 389 " --> pdb=" O CYS B 373 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 375 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE B 387 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 377 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR B 385 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 483 through 488 removed outlier: 4.338A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 718 " --> pdb=" O PHE B 735 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 531 through 536 removed outlier: 4.040A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 550 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 517 " --> pdb=" O PHE B 554 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 541 through 543 removed outlier: 3.500A pdb=" N PHE B 542 " --> pdb=" O VAL B 590 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 616 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 654 removed outlier: 3.658A pdb=" N GLY B 659 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 749 through 750 Processing sheet with id=AC7, first strand: chain 'B' and resid 780 through 797 removed outlier: 7.074A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 791 " --> pdb=" O VAL B1157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B1155 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 780 through 797 removed outlier: 7.074A pdb=" N ASN B 781 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE B1167 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 783 " --> pdb=" O ASP B1165 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B1165 " --> pdb=" O SER B 783 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B1163 " --> pdb=" O PRO B 785 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN B 787 " --> pdb=" O GLY B1161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 791 " --> pdb=" O VAL B1157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B1155 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B1167 " --> pdb=" O THR B1191 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B1189 " --> pdb=" O ILE B1169 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD1, first strand: chain 'B' and resid 1171 through 1174 removed outlier: 3.554A pdb=" N ILE B1178 " --> pdb=" O VAL B1174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.611A pdb=" N VAL C 47 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AD4, first strand: chain 'C' and resid 270 through 286 removed outlier: 7.153A pdb=" N VAL C 273 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 453 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER C 275 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 451 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN C 277 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 449 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU C 279 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL C 447 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL C 281 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 445 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS C 283 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 440 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 270 through 286 removed outlier: 7.153A pdb=" N VAL C 273 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 453 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER C 275 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 451 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN C 277 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 449 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU C 279 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL C 447 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N VAL C 281 " --> pdb=" O ASN C 445 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 445 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS C 283 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP C 448 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR C 463 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 450 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C 461 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU C 452 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.788A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 424 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER C 334 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 344 " --> pdb=" O ASP C 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 298 removed outlier: 6.788A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE C 424 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER C 334 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 344 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 388 " --> pdb=" O CYS C 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 483 through 488 removed outlier: 4.307A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 531 through 536 removed outlier: 4.121A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER C 511 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N SER C 552 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 513 " --> pdb=" O SER C 552 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE C 554 " --> pdb=" O VAL C 513 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 515 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ASN C 556 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 517 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N THR C 558 " --> pdb=" O VAL C 517 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA C 519 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.994A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 616 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 650 through 654 removed outlier: 3.543A pdb=" N GLY C 659 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 685 " --> pdb=" O TYR C 676 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 749 through 750 Processing sheet with id=AE4, first strand: chain 'C' and resid 780 through 797 removed outlier: 7.044A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 791 " --> pdb=" O VAL C1157 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 780 through 797 removed outlier: 7.044A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 791 " --> pdb=" O VAL C1157 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C1167 " --> pdb=" O THR C1191 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU C1189 " --> pdb=" O ILE C1169 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C1205 " --> pdb=" O VAL C1188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AE7, first strand: chain 'C' and resid 1171 through 1174 removed outlier: 3.538A pdb=" N ILE C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) 861 hydrogen bonds defined for protein. 2400 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: 6.30 Time building geometry restraints manager: 2.55 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: 7259 1.34 - 1.47: 6174 1.47 - 1.59: 10162 1.59 - 1.71: 0 1.71 - 1.84: 141 Bond restraints: 23736 Sorted by residual: bond pdb=" C ALA A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.15e+00 bond pdb=" C ALA C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 bond pdb=" C ALA B 43 " pdb=" N PRO B 44 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.12e+00 bond pdb=" CA ASN A 233 " pdb=" CB ASN A 233 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.72e-01 bond pdb=" C PRO A 942 " pdb=" N GLY A 943 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.64e-01 ... (remaining 23731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 31619 1.70 - 3.41: 555 3.41 - 5.11: 79 5.11 - 6.82: 17 6.82 - 8.52: 7 Bond angle restraints: 32277 Sorted by residual: angle pdb=" C ALA B 232 " pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ALA A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C ALA C 232 " pdb=" N ASN C 233 " pdb=" CA ASN C 233 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C ILE B1223 " pdb=" N GLU B1224 " pdb=" CA GLU B1224 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ILE C1223 " pdb=" N GLU C1224 " pdb=" CA GLU C1224 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.11e+01 ... (remaining 32272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 13673 17.75 - 35.50: 790 35.50 - 53.25: 102 53.25 - 71.00: 64 71.00 - 88.75: 23 Dihedral angle restraints: 14652 sinusoidal: 6132 harmonic: 8520 Sorted by residual: dihedral pdb=" CB CYS B 283 " pdb=" SG CYS B 283 " pdb=" SG CYS B 307 " pdb=" CB CYS B 307 " ideal model delta sinusoidal sigma weight residual 93.00 164.82 -71.82 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CB CYS A 283 " pdb=" SG CYS A 283 " pdb=" SG CYS A 307 " pdb=" CB CYS A 307 " ideal model delta sinusoidal sigma weight residual 93.00 164.07 -71.07 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS C 283 " pdb=" SG CYS C 283 " pdb=" SG CYS C 307 " pdb=" CB CYS C 307 " ideal model delta sinusoidal sigma weight residual 93.00 163.25 -70.25 1 1.00e+01 1.00e-02 6.36e+01 ... (remaining 14649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2631 0.038 - 0.076: 887 0.076 - 0.115: 328 0.115 - 0.153: 74 0.153 - 0.191: 13 Chirality restraints: 3933 Sorted by residual: chirality pdb=" CB ILE C1140 " pdb=" CA ILE C1140 " pdb=" CG1 ILE C1140 " pdb=" CG2 ILE C1140 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" C1 NAG C1407 " pdb=" ND2 ASN C 787 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CB ILE B1140 " pdb=" CA ILE B1140 " pdb=" CG1 ILE B1140 " pdb=" CG2 ILE B1140 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 3930 not shown) Planarity restraints: 4077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 277 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A 278 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 277 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO C 278 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 278 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 278 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 277 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 278 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 278 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 278 " -0.025 5.00e-02 4.00e+02 ... (remaining 4074 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11145 2.98 - 3.46: 21548 3.46 - 3.94: 36602 3.94 - 4.42: 40605 4.42 - 4.90: 68249 Nonbonded interactions: 178149 Sorted by model distance: nonbonded pdb=" O5 MAN I 4 " pdb=" O6 MAN I 4 " model vdw 2.504 2.432 nonbonded pdb=" O5 MAN F 5 " pdb=" O6 MAN F 5 " model vdw 2.584 2.432 nonbonded pdb=" O5 MAN I 5 " pdb=" O6 MAN I 5 " model vdw 2.619 2.432 nonbonded pdb=" N GLN A 996 " pdb=" N GLN A 997 " model vdw 2.621 2.560 nonbonded pdb=" N TYR C 751 " pdb=" O TYR C 751 " model vdw 2.625 2.496 ... (remaining 178144 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.780 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.003 0.028 23826 Z= 0.123 Angle : 0.585 8.524 32508 Z= 0.296 Chirality : 0.045 0.191 3933 Planarity : 0.004 0.046 4044 Dihedral : 11.928 88.754 9051 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2844 helix: 0.74 (0.20), residues: 633 sheet: -0.50 (0.21), residues: 684 loop : -0.85 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 919 TYR 0.016 0.001 TYR C 953 PHE 0.014 0.001 PHE B 643 TRP 0.008 0.001 TRP B 259 HIS 0.003 0.001 HIS B1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (23736) covalent geometry : angle 0.57264 / 0.29 (32277) SS BOND : bond 0.00188 / 0.13 ( 39) SS BOND : angle 1.46305 / 1.00 ( 78) hydrogen bonds : bond 0.20245 / 13.49 ( 818) hydrogen bonds : angle 8.43863 / 5.70 ( 2400) link_ALPHA1-3 : bond 0.00982 / 0.49 ( 3) link_ALPHA1-3 : angle 1.23027 / 0.89 ( 9) link_ALPHA1-6 : bond 0.01135 / 0.57 ( 3) link_ALPHA1-6 : angle 1.41478 / 1.07 ( 9) link_BETA1-4 : bond 0.00393 / 0.25 ( 12) link_BETA1-4 : angle 1.68832 / 1.31 ( 36) link_NAG-ASN : bond 0.00214 / 0.13 ( 33) link_NAG-ASN : angle 1.56858 / 1.07 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 825 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.7395 (m-80) cc_final: 0.7065 (m-80) REVERT: A 212 TYR cc_start: 0.7895 (m-80) cc_final: 0.7628 (m-10) REVERT: A 214 MET cc_start: 0.7386 (tpt) cc_final: 0.6807 (tpt) REVERT: A 247 ASN cc_start: 0.7909 (p0) cc_final: 0.7320 (t0) REVERT: A 258 ASN cc_start: 0.6415 (m-40) cc_final: 0.4671 (m-40) REVERT: A 280 LEU cc_start: 0.8519 (tp) cc_final: 0.8256 (tt) REVERT: A 301 GLN cc_start: 0.7152 (mm110) cc_final: 0.6716 (mm110) REVERT: A 388 LEU cc_start: 0.8534 (mt) cc_final: 0.8302 (mp) REVERT: A 396 ARG cc_start: 0.7633 (mtp85) cc_final: 0.6976 (mtp85) REVERT: A 466 ASP cc_start: 0.6749 (m-30) cc_final: 0.6349 (m-30) REVERT: A 472 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7827 (mttt) REVERT: A 499 ILE cc_start: 0.8167 (mm) cc_final: 0.7855 (mt) REVERT: A 509 ASP cc_start: 0.7032 (t0) cc_final: 0.6823 (t0) REVERT: A 537 ASN cc_start: 0.7475 (m-40) cc_final: 0.7236 (m110) REVERT: A 577 GLN cc_start: 0.7367 (mp-120) cc_final: 0.7167 (tp40) REVERT: A 587 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7572 (ttpp) REVERT: A 601 ILE cc_start: 0.7801 (mt) cc_final: 0.7349 (tt) REVERT: A 621 GLN cc_start: 0.7674 (tt0) cc_final: 0.7448 (tt0) REVERT: A 631 THR cc_start: 0.7547 (m) cc_final: 0.7227 (p) REVERT: A 740 ASP cc_start: 0.7785 (t0) cc_final: 0.7553 (t0) REVERT: A 758 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8140 (ttmm) REVERT: A 768 GLN cc_start: 0.7899 (mt0) cc_final: 0.7678 (mt0) REVERT: A 791 SER cc_start: 0.8460 (t) cc_final: 0.8138 (m) REVERT: A 814 ASN cc_start: 0.8692 (t0) cc_final: 0.8055 (t0) REVERT: A 820 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7568 (mmtp) REVERT: A 856 GLU cc_start: 0.7469 (tp30) cc_final: 0.7264 (tp30) REVERT: A 872 TYR cc_start: 0.8517 (m-80) cc_final: 0.8046 (m-80) REVERT: A 876 ASN cc_start: 0.8266 (m-40) cc_final: 0.8009 (m-40) REVERT: A 878 LEU cc_start: 0.7840 (mt) cc_final: 0.7601 (mt) REVERT: A 949 LYS cc_start: 0.7774 (tttt) cc_final: 0.7359 (ttmt) REVERT: A 954 SER cc_start: 0.8594 (m) cc_final: 0.8182 (p) REVERT: A 999 LEU cc_start: 0.8159 (mt) cc_final: 0.7543 (mp) REVERT: A 1010 MET cc_start: 0.7104 (ttp) cc_final: 0.6902 (ttp) REVERT: A 1058 HIS cc_start: 0.8581 (m-70) cc_final: 0.8230 (m-70) REVERT: A 1084 ASP cc_start: 0.7343 (t70) cc_final: 0.7068 (t0) REVERT: A 1113 LYS cc_start: 0.7551 (mtpp) cc_final: 0.7204 (mtpp) REVERT: A 1118 LYS cc_start: 0.7919 (mmtp) cc_final: 0.7669 (mttm) REVERT: A 1124 LYS cc_start: 0.8214 (mttt) cc_final: 0.7989 (mttp) REVERT: A 1184 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7162 (mm-30) REVERT: B 217 VAL cc_start: 0.8466 (t) cc_final: 0.8254 (t) REVERT: B 245 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 247 ASN cc_start: 0.7823 (p0) cc_final: 0.7611 (t0) REVERT: B 348 VAL cc_start: 0.7929 (m) cc_final: 0.7663 (p) REVERT: B 402 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7989 (ptmt) REVERT: B 425 ASN cc_start: 0.7592 (t0) cc_final: 0.7180 (t0) REVERT: B 464 CYS cc_start: 0.5383 (m) cc_final: 0.5082 (m) REVERT: B 472 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7613 (mttt) REVERT: B 499 ILE cc_start: 0.8414 (mm) cc_final: 0.8104 (mt) REVERT: B 506 SER cc_start: 0.8719 (t) cc_final: 0.8493 (m) REVERT: B 513 VAL cc_start: 0.8032 (t) cc_final: 0.7803 (t) REVERT: B 534 THR cc_start: 0.8498 (m) cc_final: 0.8162 (p) REVERT: B 535 THR cc_start: 0.7655 (p) cc_final: 0.7251 (t) REVERT: B 539 PHE cc_start: 0.7656 (m-80) cc_final: 0.7423 (m-80) REVERT: B 601 ILE cc_start: 0.7405 (mt) cc_final: 0.7128 (tt) REVERT: B 621 GLN cc_start: 0.7598 (tt0) cc_final: 0.7225 (tt0) REVERT: B 651 LYS cc_start: 0.8017 (tttt) cc_final: 0.7695 (ttpp) REVERT: B 677 THR cc_start: 0.8083 (m) cc_final: 0.7770 (p) REVERT: B 768 GLN cc_start: 0.7995 (mt0) cc_final: 0.7523 (mt0) REVERT: B 788 PHE cc_start: 0.8259 (m-80) cc_final: 0.8057 (m-10) REVERT: B 791 SER cc_start: 0.8622 (t) cc_final: 0.8313 (m) REVERT: B 814 ASN cc_start: 0.8665 (t0) cc_final: 0.7991 (t0) REVERT: B 820 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7774 (mtmt) REVERT: B 834 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6301 (mt-10) REVERT: B 846 VAL cc_start: 0.8690 (p) cc_final: 0.8437 (t) REVERT: B 856 GLU cc_start: 0.7522 (tp30) cc_final: 0.7275 (tp30) REVERT: B 944 VAL cc_start: 0.8508 (m) cc_final: 0.8022 (p) REVERT: B 952 MET cc_start: 0.7326 (mtm) cc_final: 0.7080 (mtm) REVERT: B 999 LEU cc_start: 0.8214 (mt) cc_final: 0.7648 (tp) REVERT: B 1003 PHE cc_start: 0.8592 (t80) cc_final: 0.8098 (t80) REVERT: B 1037 LYS cc_start: 0.8259 (tttt) cc_final: 0.7876 (ttmm) REVERT: B 1052 LEU cc_start: 0.8529 (tp) cc_final: 0.8195 (tp) REVERT: B 1084 ASP cc_start: 0.7531 (t70) cc_final: 0.7199 (t0) REVERT: B 1085 ARG cc_start: 0.7404 (ptp-110) cc_final: 0.7079 (ttm110) REVERT: B 1099 SER cc_start: 0.8273 (m) cc_final: 0.7932 (t) REVERT: B 1109 GLN cc_start: 0.7412 (mt0) cc_final: 0.7058 (mt0) REVERT: B 1211 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6486 (mm-30) REVERT: B 1221 VAL cc_start: 0.8373 (m) cc_final: 0.8053 (m) REVERT: C 38 LYS cc_start: 0.7584 (ptpt) cc_final: 0.7171 (ptpt) REVERT: C 212 TYR cc_start: 0.8171 (m-80) cc_final: 0.7650 (m-10) REVERT: C 214 MET cc_start: 0.7144 (tpt) cc_final: 0.6904 (tpt) REVERT: C 247 ASN cc_start: 0.8088 (p0) cc_final: 0.7608 (t0) REVERT: C 258 ASN cc_start: 0.6431 (m-40) cc_final: 0.5516 (m-40) REVERT: C 301 GLN cc_start: 0.7143 (mm110) cc_final: 0.6812 (mp10) REVERT: C 317 GLU cc_start: 0.7171 (pt0) cc_final: 0.6788 (pt0) REVERT: C 346 SER cc_start: 0.8638 (m) cc_final: 0.8396 (t) REVERT: C 371 TYR cc_start: 0.7870 (m-80) cc_final: 0.7562 (m-10) REVERT: C 386 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7743 (mtpp) REVERT: C 397 GLU cc_start: 0.6613 (tt0) cc_final: 0.6403 (tt0) REVERT: C 402 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8329 (ptmt) REVERT: C 462 LEU cc_start: 0.8021 (tp) cc_final: 0.7662 (tt) REVERT: C 472 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7665 (mttt) REVERT: C 487 ILE cc_start: 0.8399 (pt) cc_final: 0.8130 (tt) REVERT: C 506 SER cc_start: 0.8207 (t) cc_final: 0.7902 (m) REVERT: C 509 ASP cc_start: 0.7076 (t0) cc_final: 0.6835 (t0) REVERT: C 534 THR cc_start: 0.8546 (m) cc_final: 0.8112 (p) REVERT: C 539 PHE cc_start: 0.7493 (m-80) cc_final: 0.7132 (m-80) REVERT: C 601 ILE cc_start: 0.7762 (mt) cc_final: 0.7383 (tt) REVERT: C 616 THR cc_start: 0.8286 (t) cc_final: 0.8067 (m) REVERT: C 626 GLU cc_start: 0.6284 (mp0) cc_final: 0.5765 (mp0) REVERT: C 664 THR cc_start: 0.7221 (m) cc_final: 0.6946 (m) REVERT: C 687 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8420 (ttmt) REVERT: C 691 SER cc_start: 0.8535 (p) cc_final: 0.8276 (t) REVERT: C 748 VAL cc_start: 0.8924 (t) cc_final: 0.8619 (p) REVERT: C 765 VAL cc_start: 0.8542 (t) cc_final: 0.8293 (m) REVERT: C 788 PHE cc_start: 0.8380 (m-80) cc_final: 0.7274 (m-80) REVERT: C 789 SER cc_start: 0.8024 (p) cc_final: 0.7756 (p) REVERT: C 805 SER cc_start: 0.7943 (t) cc_final: 0.7629 (p) REVERT: C 820 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7729 (mtmt) REVERT: C 831 LYS cc_start: 0.7560 (tttt) cc_final: 0.7272 (tttm) REVERT: C 856 GLU cc_start: 0.7701 (tp30) cc_final: 0.7464 (tp30) REVERT: C 917 TYR cc_start: 0.8618 (m-80) cc_final: 0.8116 (m-80) REVERT: C 918 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8321 (mtmt) REVERT: C 999 LEU cc_start: 0.8167 (mt) cc_final: 0.7936 (mp) REVERT: C 1001 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6959 (mm-30) REVERT: C 1028 LEU cc_start: 0.7927 (mt) cc_final: 0.7640 (mt) REVERT: C 1037 LYS cc_start: 0.8219 (tttt) cc_final: 0.8004 (ttmm) REVERT: C 1064 SER cc_start: 0.7759 (t) cc_final: 0.7392 (m) REVERT: C 1084 ASP cc_start: 0.7235 (t70) cc_final: 0.6896 (t0) REVERT: C 1124 LYS cc_start: 0.8483 (mttt) cc_final: 0.8167 (mttp) REVERT: C 1164 VAL cc_start: 0.8444 (t) cc_final: 0.8015 (m) REVERT: C 1180 LEU cc_start: 0.8616 (mt) cc_final: 0.6631 (mt) REVERT: C 1208 ARG cc_start: 0.6249 (mtp180) cc_final: 0.5940 (ttm170) outliers start: 0 outliers final: 0 residues processed: 825 average time/residue: 0.1445 time to fit residues: 188.4417 Evaluate side-chains 612 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 GLN A 276 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN A1109 GLN B 228 GLN B 249 HIS B 270 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 GLN B 537 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 GLN B 705 GLN C 249 HIS ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 ASN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN C 768 GLN C 996 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097120 restraints weight = 39633.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.100322 restraints weight = 20012.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.102391 restraints weight = 11972.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103690 restraints weight = 8237.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104632 restraints weight = 6332.854| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 23826 Z= 0.259 Angle : 0.721 16.651 32508 Z= 0.361 Chirality : 0.047 0.237 3933 Planarity : 0.004 0.045 4044 Dihedral : 6.190 52.594 4164 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.59 % Allowed : 10.47 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.16), residues: 2844 helix: 1.09 (0.21), residues: 636 sheet: -0.73 (0.20), residues: 711 loop : -0.89 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.017 0.002 TYR B 676 PHE 0.020 0.002 PHE A1141 TRP 0.009 0.002 TRP B 439 HIS 0.010 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (23736) covalent geometry : angle 0.68296 / 0.35 (32277) SS BOND : bond 0.00773 / 0.43 ( 39) SS BOND : angle 2.81162 / 2.06 ( 78) hydrogen bonds : bond 0.05039 / 3.28 ( 818) hydrogen bonds : angle 6.18153 / 4.21 ( 2400) link_ALPHA1-3 : bond 0.00857 / 0.43 ( 3) link_ALPHA1-3 : angle 1.32506 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00954 / 0.47 ( 3) link_ALPHA1-6 : angle 1.05460 / 0.79 ( 9) link_BETA1-4 : bond 0.00348 / 0.22 ( 12) link_BETA1-4 : angle 1.88627 / 1.31 ( 36) link_NAG-ASN : bond 0.00985 / 0.59 ( 33) link_NAG-ASN : angle 3.31152 / 2.29 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 645 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.7623 (m-80) cc_final: 0.7340 (m-80) REVERT: A 214 MET cc_start: 0.7298 (tpt) cc_final: 0.6998 (tpp) REVERT: A 215 LEU cc_start: 0.8375 (mp) cc_final: 0.8057 (mp) REVERT: A 258 ASN cc_start: 0.6749 (m-40) cc_final: 0.4780 (m110) REVERT: A 386 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7676 (mtpp) REVERT: A 396 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7019 (mtp85) REVERT: A 448 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: A 466 ASP cc_start: 0.6495 (m-30) cc_final: 0.6223 (m-30) REVERT: A 499 ILE cc_start: 0.8156 (mm) cc_final: 0.7913 (mt) REVERT: A 509 ASP cc_start: 0.7257 (t0) cc_final: 0.6820 (t0) REVERT: A 537 ASN cc_start: 0.7658 (m-40) cc_final: 0.7446 (t0) REVERT: A 587 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7630 (ttpp) REVERT: A 614 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7848 (ptmt) REVERT: A 620 PHE cc_start: 0.8031 (m-80) cc_final: 0.7624 (m-10) REVERT: A 689 VAL cc_start: 0.8716 (t) cc_final: 0.8510 (p) REVERT: A 730 GLU cc_start: 0.6845 (tt0) cc_final: 0.6635 (tt0) REVERT: A 750 VAL cc_start: 0.8138 (t) cc_final: 0.7906 (p) REVERT: A 768 GLN cc_start: 0.8034 (mt0) cc_final: 0.7465 (mt0) REVERT: A 788 PHE cc_start: 0.7858 (m-80) cc_final: 0.7644 (m-80) REVERT: A 791 SER cc_start: 0.8427 (t) cc_final: 0.8089 (m) REVERT: A 814 ASN cc_start: 0.8805 (t0) cc_final: 0.8190 (t0) REVERT: A 820 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7430 (mttt) REVERT: A 844 GLU cc_start: 0.7369 (tp30) cc_final: 0.6968 (tp30) REVERT: A 872 TYR cc_start: 0.8618 (m-80) cc_final: 0.8203 (m-80) REVERT: A 876 ASN cc_start: 0.8327 (m-40) cc_final: 0.8055 (m-40) REVERT: A 949 LYS cc_start: 0.8085 (tttt) cc_final: 0.7270 (ttmt) REVERT: A 952 MET cc_start: 0.7693 (mtm) cc_final: 0.7024 (mpp) REVERT: A 954 SER cc_start: 0.8559 (m) cc_final: 0.8236 (p) REVERT: A 981 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7063 (mtt180) REVERT: A 999 LEU cc_start: 0.7939 (mt) cc_final: 0.7709 (mp) REVERT: A 1064 SER cc_start: 0.8213 (t) cc_final: 0.7808 (m) REVERT: A 1073 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8399 (ttm-80) REVERT: A 1074 LEU cc_start: 0.8014 (mp) cc_final: 0.7759 (mm) REVERT: A 1084 ASP cc_start: 0.7553 (t70) cc_final: 0.7297 (t0) REVERT: A 1104 LYS cc_start: 0.8250 (mmpt) cc_final: 0.7992 (tppp) REVERT: A 1108 VAL cc_start: 0.8280 (t) cc_final: 0.8055 (p) REVERT: A 1138 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6267 (mt-10) REVERT: A 1184 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 217 VAL cc_start: 0.8282 (t) cc_final: 0.8065 (t) REVERT: B 245 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6883 (mt-10) REVERT: B 247 ASN cc_start: 0.7805 (p0) cc_final: 0.7574 (p0) REVERT: B 257 ASN cc_start: 0.7400 (t0) cc_final: 0.7087 (t0) REVERT: B 264 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7161 (t0) REVERT: B 282 ASN cc_start: 0.8034 (m110) cc_final: 0.7644 (m-40) REVERT: B 372 TYR cc_start: 0.7575 (m-10) cc_final: 0.7355 (m-80) REVERT: B 386 LYS cc_start: 0.8505 (mtpt) cc_final: 0.8109 (mtpt) REVERT: B 420 ASP cc_start: 0.7686 (p0) cc_final: 0.7171 (t0) REVERT: B 481 ASP cc_start: 0.7316 (m-30) cc_final: 0.6807 (p0) REVERT: B 506 SER cc_start: 0.8744 (t) cc_final: 0.8336 (m) REVERT: B 509 ASP cc_start: 0.7507 (t0) cc_final: 0.7242 (t0) REVERT: B 512 PHE cc_start: 0.7868 (m-80) cc_final: 0.7636 (m-80) REVERT: B 537 ASN cc_start: 0.7589 (m-40) cc_final: 0.6840 (t0) REVERT: B 595 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7293 (tp) REVERT: B 614 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7344 (ptmm) REVERT: B 617 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8267 (m) REVERT: B 621 GLN cc_start: 0.7446 (tt0) cc_final: 0.7122 (tt0) REVERT: B 640 ASP cc_start: 0.7532 (t0) cc_final: 0.7086 (t0) REVERT: B 651 LYS cc_start: 0.8036 (tttt) cc_final: 0.7768 (ttpp) REVERT: B 682 GLN cc_start: 0.6670 (mp10) cc_final: 0.5973 (mp10) REVERT: B 704 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6542 (mt-10) REVERT: B 736 TYR cc_start: 0.8217 (t80) cc_final: 0.7940 (t80) REVERT: B 768 GLN cc_start: 0.8101 (mt0) cc_final: 0.7550 (mt0) REVERT: B 791 SER cc_start: 0.8463 (t) cc_final: 0.7958 (m) REVERT: B 814 ASN cc_start: 0.8848 (t0) cc_final: 0.8159 (t0) REVERT: B 820 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7863 (mtpp) REVERT: B 834 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6579 (mt-10) REVERT: B 944 VAL cc_start: 0.8839 (m) cc_final: 0.8406 (p) REVERT: B 1005 SER cc_start: 0.8438 (m) cc_final: 0.8174 (m) REVERT: B 1037 LYS cc_start: 0.8249 (tttt) cc_final: 0.8006 (tptp) REVERT: B 1051 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6887 (mm-40) REVERT: B 1052 LEU cc_start: 0.8303 (tp) cc_final: 0.8015 (tp) REVERT: B 1084 ASP cc_start: 0.7701 (t70) cc_final: 0.7384 (t0) REVERT: B 1099 SER cc_start: 0.8160 (m) cc_final: 0.7930 (t) REVERT: B 1104 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7930 (mtpt) REVERT: B 1109 GLN cc_start: 0.7398 (mt0) cc_final: 0.7181 (mt0) REVERT: B 1120 ASN cc_start: 0.7852 (m-40) cc_final: 0.7621 (m-40) REVERT: C 38 LYS cc_start: 0.7915 (ptpt) cc_final: 0.7379 (ptpt) REVERT: C 212 TYR cc_start: 0.8089 (m-80) cc_final: 0.7551 (m-10) REVERT: C 266 SER cc_start: 0.7825 (m) cc_final: 0.7583 (p) REVERT: C 301 GLN cc_start: 0.7191 (mm110) cc_final: 0.6656 (mm110) REVERT: C 346 SER cc_start: 0.8515 (m) cc_final: 0.8163 (t) REVERT: C 371 TYR cc_start: 0.7751 (m-80) cc_final: 0.7481 (m-10) REVERT: C 386 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7522 (mtpp) REVERT: C 388 LEU cc_start: 0.8672 (mt) cc_final: 0.8468 (mt) REVERT: C 452 GLU cc_start: 0.7582 (tt0) cc_final: 0.7345 (tt0) REVERT: C 462 LEU cc_start: 0.8279 (tp) cc_final: 0.7923 (tt) REVERT: C 472 LYS cc_start: 0.7892 (mtpt) cc_final: 0.7534 (mttt) REVERT: C 487 ILE cc_start: 0.8007 (pt) cc_final: 0.7778 (tt) REVERT: C 506 SER cc_start: 0.8342 (t) cc_final: 0.7788 (m) REVERT: C 509 ASP cc_start: 0.7065 (t0) cc_final: 0.6764 (t0) REVERT: C 539 PHE cc_start: 0.7496 (m-80) cc_final: 0.7223 (m-80) REVERT: C 616 THR cc_start: 0.8294 (t) cc_final: 0.8060 (m) REVERT: C 626 GLU cc_start: 0.6555 (mp0) cc_final: 0.5974 (mp0) REVERT: C 664 THR cc_start: 0.7307 (m) cc_final: 0.6800 (t) REVERT: C 691 SER cc_start: 0.8688 (p) cc_final: 0.8457 (t) REVERT: C 704 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6992 (mt-10) REVERT: C 748 VAL cc_start: 0.8931 (t) cc_final: 0.8581 (p) REVERT: C 765 VAL cc_start: 0.8515 (t) cc_final: 0.8272 (m) REVERT: C 788 PHE cc_start: 0.7887 (m-80) cc_final: 0.7665 (m-80) REVERT: C 789 SER cc_start: 0.7978 (p) cc_final: 0.7669 (p) REVERT: C 805 SER cc_start: 0.8067 (t) cc_final: 0.7608 (p) REVERT: C 820 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7768 (mtmt) REVERT: C 856 GLU cc_start: 0.7447 (tp30) cc_final: 0.7246 (mm-30) REVERT: C 918 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8388 (mtmt) REVERT: C 1037 LYS cc_start: 0.8333 (tttt) cc_final: 0.8102 (ttmm) REVERT: C 1064 SER cc_start: 0.8009 (t) cc_final: 0.7558 (m) REVERT: C 1073 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: C 1074 LEU cc_start: 0.8203 (mt) cc_final: 0.7864 (mm) REVERT: C 1084 ASP cc_start: 0.7428 (t70) cc_final: 0.7158 (t0) REVERT: C 1159 VAL cc_start: 0.8462 (t) cc_final: 0.8152 (m) REVERT: C 1164 VAL cc_start: 0.8414 (t) cc_final: 0.8007 (m) REVERT: C 1208 ARG cc_start: 0.6402 (mtp180) cc_final: 0.6074 (ttm170) REVERT: C 1221 VAL cc_start: 0.8237 (m) cc_final: 0.8015 (t) outliers start: 66 outliers final: 44 residues processed: 674 average time/residue: 0.1453 time to fit residues: 156.5053 Evaluate side-chains 635 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 587 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1108 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1126 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN C 768 GLN ** C 933 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 = 0.3413 r_free = 0.3413 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097511 restraints weight = 39451.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.100702 restraints weight = 19699.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102769 restraints weight = 11706.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104103 restraints weight = 7971.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105018 restraints weight = 6060.840| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 23826 Z= 0.170 Angle : 0.657 14.505 32508 Z= 0.327 Chirality : 0.045 0.235 3933 Planarity : 0.004 0.058 4044 Dihedral : 6.060 54.024 4164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.18 % Allowed : 13.61 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2844 helix: 1.26 (0.20), residues: 654 sheet: -0.54 (0.21), residues: 666 loop : -1.00 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.024 0.002 TYR B 676 PHE 0.016 0.001 PHE B 585 TRP 0.005 0.001 TRP A 439 HIS 0.008 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (23736) covalent geometry : angle 0.61882 / 0.31 (32277) SS BOND : bond 0.00546 / 0.32 ( 39) SS BOND : angle 3.08335 / 1.96 ( 78) hydrogen bonds : bond 0.04428 / 2.88 ( 818) hydrogen bonds : angle 5.74615 / 3.90 ( 2400) link_ALPHA1-3 : bond 0.00887 / 0.45 ( 3) link_ALPHA1-3 : angle 1.05612 / 0.70 ( 9) link_ALPHA1-6 : bond 0.00968 / 0.48 ( 3) link_ALPHA1-6 : angle 1.23144 / 0.92 ( 9) link_BETA1-4 : bond 0.00330 / 0.22 ( 12) link_BETA1-4 : angle 1.64436 / 1.20 ( 36) link_NAG-ASN : bond 0.00773 / 0.47 ( 33) link_NAG-ASN : angle 2.82579 / 1.96 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 603 time to evaluate : 0.837 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: A 81 PHE cc_start: 0.7649 (m-80) cc_final: 0.7401 (m-80) REVERT: A 215 LEU cc_start: 0.8399 (mp) cc_final: 0.8010 (mt) REVERT: A 245 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: A 247 ASN cc_start: 0.7813 (p0) cc_final: 0.7592 (p0) REVERT: A 386 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7694 (mttm) REVERT: A 448 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: A 466 ASP cc_start: 0.6392 (m-30) cc_final: 0.6105 (m-30) REVERT: A 499 ILE cc_start: 0.8172 (mm) cc_final: 0.7905 (mt) REVERT: A 509 ASP cc_start: 0.7143 (t0) cc_final: 0.6787 (t0) REVERT: A 614 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7748 (ptmt) REVERT: A 620 PHE cc_start: 0.8079 (m-80) cc_final: 0.7647 (m-10) REVERT: A 748 VAL cc_start: 0.8831 (t) cc_final: 0.8622 (p) REVERT: A 750 VAL cc_start: 0.8100 (t) cc_final: 0.7835 (p) REVERT: A 768 GLN cc_start: 0.7988 (mt0) cc_final: 0.7471 (mt0) REVERT: A 814 ASN cc_start: 0.8831 (t0) cc_final: 0.8215 (t0) REVERT: A 820 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7506 (mttt) REVERT: A 872 TYR cc_start: 0.8516 (m-80) cc_final: 0.8229 (m-80) REVERT: A 876 ASN cc_start: 0.8266 (m-40) cc_final: 0.8021 (m-40) REVERT: A 918 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8253 (mtpp) REVERT: A 954 SER cc_start: 0.8577 (m) cc_final: 0.8252 (p) REVERT: A 1064 SER cc_start: 0.8174 (t) cc_final: 0.7780 (m) REVERT: A 1074 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7858 (mm) REVERT: A 1104 LYS cc_start: 0.8280 (mmpt) cc_final: 0.7967 (tppp) REVERT: A 1138 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6344 (mt-10) REVERT: A 1164 VAL cc_start: 0.8355 (t) cc_final: 0.8089 (m) REVERT: A 1184 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 1213 ARG cc_start: 0.7864 (ptt90) cc_final: 0.7425 (ptt-90) REVERT: B 42 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6917 (mm110) REVERT: B 217 VAL cc_start: 0.8332 (t) cc_final: 0.8109 (t) REVERT: B 247 ASN cc_start: 0.7869 (p0) cc_final: 0.7621 (p0) REVERT: B 257 ASN cc_start: 0.7306 (t0) cc_final: 0.7008 (t0) REVERT: B 264 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6799 (t0) REVERT: B 282 ASN cc_start: 0.8149 (m110) cc_final: 0.7843 (m-40) REVERT: B 284 LEU cc_start: 0.8135 (tp) cc_final: 0.7842 (tt) REVERT: B 317 GLU cc_start: 0.7318 (pt0) cc_final: 0.7009 (pm20) REVERT: B 386 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8105 (mtpt) REVERT: B 420 ASP cc_start: 0.7724 (p0) cc_final: 0.7128 (t0) REVERT: B 445 ASN cc_start: 0.7080 (m110) cc_final: 0.6830 (m-40) REVERT: B 452 GLU cc_start: 0.7468 (tt0) cc_final: 0.7178 (tt0) REVERT: B 506 SER cc_start: 0.8723 (t) cc_final: 0.8320 (m) REVERT: B 509 ASP cc_start: 0.7556 (t0) cc_final: 0.7253 (t0) REVERT: B 537 ASN cc_start: 0.7494 (m-40) cc_final: 0.6633 (t0) REVERT: B 545 ASP cc_start: 0.8117 (p0) cc_final: 0.7602 (p0) REVERT: B 640 ASP cc_start: 0.7508 (t0) cc_final: 0.6970 (t0) REVERT: B 651 LYS cc_start: 0.8001 (tttt) cc_final: 0.7759 (ttpp) REVERT: B 704 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6388 (mt-10) REVERT: B 736 TYR cc_start: 0.8222 (t80) cc_final: 0.7964 (t80) REVERT: B 768 GLN cc_start: 0.8063 (mt0) cc_final: 0.7517 (mt0) REVERT: B 814 ASN cc_start: 0.8838 (t0) cc_final: 0.8147 (t0) REVERT: B 820 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7805 (mtpp) REVERT: B 831 LYS cc_start: 0.7879 (tptm) cc_final: 0.7646 (tmtt) REVERT: B 944 VAL cc_start: 0.8754 (m) cc_final: 0.8360 (p) REVERT: B 1005 SER cc_start: 0.8353 (m) cc_final: 0.8072 (m) REVERT: B 1037 LYS cc_start: 0.8209 (tttt) cc_final: 0.8008 (tptp) REVERT: B 1051 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6853 (mm-40) REVERT: B 1052 LEU cc_start: 0.8244 (tp) cc_final: 0.7942 (tp) REVERT: B 1084 ASP cc_start: 0.7701 (t70) cc_final: 0.7406 (t0) REVERT: B 1099 SER cc_start: 0.8304 (m) cc_final: 0.8061 (t) REVERT: B 1104 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7877 (ttmm) REVERT: B 1120 ASN cc_start: 0.7874 (m-40) cc_final: 0.7514 (m-40) REVERT: C 38 LYS cc_start: 0.7855 (ptpt) cc_final: 0.7369 (ptpt) REVERT: C 212 TYR cc_start: 0.8001 (m-80) cc_final: 0.7501 (m-10) REVERT: C 247 ASN cc_start: 0.8123 (p0) cc_final: 0.6928 (p0) REVERT: C 249 HIS cc_start: 0.7595 (m-70) cc_final: 0.7057 (m170) REVERT: C 258 ASN cc_start: 0.6802 (m-40) cc_final: 0.6004 (m-40) REVERT: C 266 SER cc_start: 0.7836 (m) cc_final: 0.7587 (p) REVERT: C 301 GLN cc_start: 0.7206 (mm110) cc_final: 0.6489 (mm-40) REVERT: C 346 SER cc_start: 0.8538 (m) cc_final: 0.8185 (t) REVERT: C 348 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 386 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7702 (mttm) REVERT: C 388 LEU cc_start: 0.8660 (mt) cc_final: 0.8265 (mt) REVERT: C 397 GLU cc_start: 0.6673 (tt0) cc_final: 0.6401 (tt0) REVERT: C 450 LEU cc_start: 0.7915 (tp) cc_final: 0.7671 (tp) REVERT: C 462 LEU cc_start: 0.8163 (tp) cc_final: 0.7867 (tt) REVERT: C 470 GLN cc_start: 0.7756 (tp40) cc_final: 0.7415 (tt0) REVERT: C 472 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7519 (mttt) REVERT: C 506 SER cc_start: 0.8342 (t) cc_final: 0.7784 (m) REVERT: C 509 ASP cc_start: 0.7062 (t0) cc_final: 0.6755 (t0) REVERT: C 539 PHE cc_start: 0.7452 (m-80) cc_final: 0.7249 (m-80) REVERT: C 664 THR cc_start: 0.7239 (m) cc_final: 0.6695 (t) REVERT: C 687 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8378 (ttmt) REVERT: C 691 SER cc_start: 0.8654 (p) cc_final: 0.8453 (t) REVERT: C 704 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6810 (mt-10) REVERT: C 748 VAL cc_start: 0.8959 (t) cc_final: 0.8613 (p) REVERT: C 765 VAL cc_start: 0.8525 (t) cc_final: 0.8252 (m) REVERT: C 788 PHE cc_start: 0.7929 (m-80) cc_final: 0.7664 (m-80) REVERT: C 795 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 805 SER cc_start: 0.8115 (t) cc_final: 0.7515 (p) REVERT: C 821 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7277 (mm-40) REVERT: C 847 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: C 900 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7965 (tt) REVERT: C 918 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8498 (mtmt) REVERT: C 1064 SER cc_start: 0.8031 (t) cc_final: 0.7539 (m) REVERT: C 1084 ASP cc_start: 0.7390 (t70) cc_final: 0.7139 (t0) REVERT: C 1164 VAL cc_start: 0.8395 (t) cc_final: 0.8033 (m) REVERT: C 1208 ARG cc_start: 0.6352 (mtp180) cc_final: 0.5991 (ttm170) REVERT: C 1221 VAL cc_start: 0.8233 (m) cc_final: 0.8021 (t) outliers start: 81 outliers final: 50 residues processed: 641 average time/residue: 0.1465 time to fit residues: 149.6587 Evaluate side-chains 624 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 566 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1218 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 222 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN B 282 ASN B 454 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN ** C 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.102849 restraints weight = 37838.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106263 restraints weight = 19039.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108435 restraints weight = 11390.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109803 restraints weight = 7780.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110790 restraints weight = 5962.937| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23826 Z= 0.181 Angle : 0.639 11.403 32508 Z= 0.318 Chirality : 0.045 0.225 3933 Planarity : 0.004 0.057 4044 Dihedral : 6.042 53.505 4164 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.61 % Allowed : 14.67 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.16), residues: 2844 helix: 1.32 (0.21), residues: 648 sheet: -0.52 (0.20), residues: 666 loop : -1.09 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 547 TYR 0.025 0.002 TYR B 676 PHE 0.018 0.002 PHE A1141 TRP 0.007 0.001 TRP A 439 HIS 0.009 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (23736) covalent geometry : angle 0.60640 / 0.31 (32277) SS BOND : bond 0.00531 / 0.31 ( 39) SS BOND : angle 2.71276 / 1.83 ( 78) hydrogen bonds : bond 0.04294 / 2.77 ( 818) hydrogen bonds : angle 5.51393 / 3.73 ( 2400) link_ALPHA1-3 : bond 0.01065 / 0.53 ( 3) link_ALPHA1-3 : angle 1.18928 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00967 / 0.48 ( 3) link_ALPHA1-6 : angle 1.22074 / 0.92 ( 9) link_BETA1-4 : bond 0.00344 / 0.21 ( 12) link_BETA1-4 : angle 1.67564 / 1.22 ( 36) link_NAG-ASN : bond 0.00557 / 0.33 ( 33) link_NAG-ASN : angle 2.62647 / 1.79 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 584 time to evaluate : 0.782 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: A 81 PHE cc_start: 0.7543 (m-80) cc_final: 0.7336 (m-80) REVERT: A 215 LEU cc_start: 0.8578 (mp) cc_final: 0.8082 (mt) REVERT: A 247 ASN cc_start: 0.7921 (p0) cc_final: 0.7705 (p0) REVERT: A 386 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7808 (mtpp) REVERT: A 448 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: A 499 ILE cc_start: 0.8173 (mm) cc_final: 0.7865 (mt) REVERT: A 509 ASP cc_start: 0.6930 (t0) cc_final: 0.6695 (t0) REVERT: A 602 ASP cc_start: 0.7534 (m-30) cc_final: 0.7283 (m-30) REVERT: A 614 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7753 (ptmt) REVERT: A 620 PHE cc_start: 0.8006 (m-80) cc_final: 0.7593 (m-10) REVERT: A 748 VAL cc_start: 0.8921 (t) cc_final: 0.8682 (p) REVERT: A 750 VAL cc_start: 0.8116 (t) cc_final: 0.7868 (p) REVERT: A 768 GLN cc_start: 0.7901 (mt0) cc_final: 0.7400 (mt0) REVERT: A 788 PHE cc_start: 0.7768 (m-80) cc_final: 0.7409 (m-80) REVERT: A 820 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7491 (mttt) REVERT: A 872 TYR cc_start: 0.8418 (m-80) cc_final: 0.8194 (m-80) REVERT: A 918 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8522 (mtpp) REVERT: A 945 VAL cc_start: 0.8481 (p) cc_final: 0.8162 (t) REVERT: A 954 SER cc_start: 0.8536 (m) cc_final: 0.8185 (p) REVERT: A 1064 SER cc_start: 0.8067 (t) cc_final: 0.7647 (m) REVERT: A 1074 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7854 (mm) REVERT: A 1104 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7977 (tppp) REVERT: A 1109 GLN cc_start: 0.7770 (tt0) cc_final: 0.7535 (tt0) REVERT: A 1164 VAL cc_start: 0.8313 (t) cc_final: 0.8081 (m) REVERT: A 1184 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 1213 ARG cc_start: 0.7808 (ptt180) cc_final: 0.7310 (ptt-90) REVERT: A 1219 ASP cc_start: 0.8212 (m-30) cc_final: 0.7948 (m-30) REVERT: B 38 LYS cc_start: 0.7478 (ptpt) cc_final: 0.7135 (ptpt) REVERT: B 42 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7166 (mm110) REVERT: B 217 VAL cc_start: 0.8464 (t) cc_final: 0.8233 (t) REVERT: B 264 ASN cc_start: 0.6884 (OUTLIER) cc_final: 0.6068 (t0) REVERT: B 284 LEU cc_start: 0.8094 (tp) cc_final: 0.7782 (tt) REVERT: B 317 GLU cc_start: 0.7048 (pt0) cc_final: 0.6730 (pm20) REVERT: B 386 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8235 (mtpt) REVERT: B 387 PHE cc_start: 0.8609 (t80) cc_final: 0.8255 (t80) REVERT: B 420 ASP cc_start: 0.7752 (p0) cc_final: 0.7086 (t0) REVERT: B 445 ASN cc_start: 0.7100 (m110) cc_final: 0.6641 (m110) REVERT: B 506 SER cc_start: 0.8676 (t) cc_final: 0.8374 (m) REVERT: B 509 ASP cc_start: 0.7479 (t0) cc_final: 0.7240 (t0) REVERT: B 537 ASN cc_start: 0.7397 (m-40) cc_final: 0.6607 (t0) REVERT: B 545 ASP cc_start: 0.7908 (p0) cc_final: 0.7535 (p0) REVERT: B 640 ASP cc_start: 0.7428 (t0) cc_final: 0.6816 (t0) REVERT: B 651 LYS cc_start: 0.8064 (tttt) cc_final: 0.7707 (ttpp) REVERT: B 704 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 730 GLU cc_start: 0.7146 (tp30) cc_final: 0.6847 (tp30) REVERT: B 736 TYR cc_start: 0.8189 (t80) cc_final: 0.7965 (t80) REVERT: B 750 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7869 (p) REVERT: B 768 GLN cc_start: 0.7972 (mt0) cc_final: 0.7497 (mt0) REVERT: B 777 MET cc_start: 0.7129 (mmm) cc_final: 0.6773 (mmm) REVERT: B 814 ASN cc_start: 0.8853 (t0) cc_final: 0.8219 (t0) REVERT: B 820 LYS cc_start: 0.8050 (mtmt) cc_final: 0.7804 (mtpp) REVERT: B 850 SER cc_start: 0.8602 (t) cc_final: 0.8283 (p) REVERT: B 944 VAL cc_start: 0.8757 (m) cc_final: 0.8445 (p) REVERT: B 1005 SER cc_start: 0.8383 (m) cc_final: 0.8112 (m) REVERT: B 1051 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6808 (mm-40) REVERT: B 1052 LEU cc_start: 0.8380 (tp) cc_final: 0.8016 (tp) REVERT: B 1084 ASP cc_start: 0.7599 (t70) cc_final: 0.7298 (t0) REVERT: B 1099 SER cc_start: 0.8504 (m) cc_final: 0.8220 (t) REVERT: B 1104 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7967 (ttmm) REVERT: B 1218 SER cc_start: 0.8263 (m) cc_final: 0.7627 (p) REVERT: C 38 LYS cc_start: 0.7655 (ptpt) cc_final: 0.7181 (ptpt) REVERT: C 247 ASN cc_start: 0.8102 (p0) cc_final: 0.7825 (p0) REVERT: C 258 ASN cc_start: 0.6591 (m-40) cc_final: 0.5465 (m-40) REVERT: C 266 SER cc_start: 0.7907 (m) cc_final: 0.7619 (p) REVERT: C 303 ILE cc_start: 0.8253 (mm) cc_final: 0.8009 (tt) REVERT: C 346 SER cc_start: 0.8583 (m) cc_final: 0.8370 (t) REVERT: C 348 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7251 (p) REVERT: C 386 LYS cc_start: 0.8068 (mtpt) cc_final: 0.7816 (mttm) REVERT: C 388 LEU cc_start: 0.8462 (mt) cc_final: 0.8243 (mt) REVERT: C 450 LEU cc_start: 0.8006 (tp) cc_final: 0.7758 (tp) REVERT: C 462 LEU cc_start: 0.8172 (tp) cc_final: 0.7938 (tt) REVERT: C 470 GLN cc_start: 0.7355 (tp40) cc_final: 0.7110 (tt0) REVERT: C 506 SER cc_start: 0.8388 (t) cc_final: 0.7760 (m) REVERT: C 651 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7512 (ttpp) REVERT: C 664 THR cc_start: 0.7290 (m) cc_final: 0.6851 (t) REVERT: C 691 SER cc_start: 0.8667 (p) cc_final: 0.8300 (t) REVERT: C 704 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6450 (mt-10) REVERT: C 739 ASN cc_start: 0.8170 (m-40) cc_final: 0.7966 (m-40) REVERT: C 748 VAL cc_start: 0.8981 (t) cc_final: 0.8641 (p) REVERT: C 765 VAL cc_start: 0.8463 (t) cc_final: 0.8193 (m) REVERT: C 788 PHE cc_start: 0.8119 (m-80) cc_final: 0.7458 (m-80) REVERT: C 805 SER cc_start: 0.8168 (t) cc_final: 0.7586 (p) REVERT: C 821 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7177 (mm-40) REVERT: C 847 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: C 900 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8107 (tt) REVERT: C 918 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8596 (mtmm) REVERT: C 1064 SER cc_start: 0.7946 (t) cc_final: 0.7424 (m) REVERT: C 1084 ASP cc_start: 0.7340 (t70) cc_final: 0.7056 (t0) REVERT: C 1104 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7920 (tppp) REVERT: C 1164 VAL cc_start: 0.8482 (t) cc_final: 0.8180 (m) REVERT: C 1208 ARG cc_start: 0.6079 (mtp180) cc_final: 0.5751 (ttm170) outliers start: 92 outliers final: 59 residues processed: 633 average time/residue: 0.1452 time to fit residues: 148.1210 Evaluate side-chains 622 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 554 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 228 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 CYS Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 1104 LYS Chi-restraints excluded: chain C residue 1108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 218 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 202 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 289 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 ASN B 988 GLN B1109 GLN C 228 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 933 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 = 0.3502 r_free = 0.3502 target = 0.120071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102687 restraints weight = 37741.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106094 restraints weight = 18672.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108283 restraints weight = 10974.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109648 restraints weight = 7392.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110636 restraints weight = 5639.077| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23826 Z= 0.163 Angle : 0.638 15.579 32508 Z= 0.319 Chirality : 0.045 0.251 3933 Planarity : 0.004 0.058 4044 Dihedral : 6.035 54.208 4164 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.76 % Allowed : 16.24 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2844 helix: 1.37 (0.21), residues: 648 sheet: -0.34 (0.20), residues: 654 loop : -1.15 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.022 0.001 TYR B 676 PHE 0.016 0.001 PHE A1141 TRP 0.006 0.001 TRP A 439 HIS 0.005 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (23736) covalent geometry : angle 0.60165 / 0.31 (32277) SS BOND : bond 0.00498 / 0.29 ( 39) SS BOND : angle 3.15314 / 2.03 ( 78) hydrogen bonds : bond 0.04174 / 2.69 ( 818) hydrogen bonds : angle 5.37616 / 3.64 ( 2400) link_ALPHA1-3 : bond 0.01017 / 0.51 ( 3) link_ALPHA1-3 : angle 1.15378 / 0.80 ( 9) link_ALPHA1-6 : bond 0.01172 / 0.59 ( 3) link_ALPHA1-6 : angle 1.30595 / 0.99 ( 9) link_BETA1-4 : bond 0.00386 / 0.22 ( 12) link_BETA1-4 : angle 1.64452 / 1.21 ( 36) link_NAG-ASN : bond 0.00495 / 0.30 ( 33) link_NAG-ASN : angle 2.57605 / 1.75 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 576 time to evaluate : 0.853 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: A 212 TYR cc_start: 0.7612 (m-80) cc_final: 0.7376 (m-10) REVERT: A 215 LEU cc_start: 0.8447 (mp) cc_final: 0.8215 (mp) REVERT: A 228 GLN cc_start: 0.7387 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 247 ASN cc_start: 0.7961 (p0) cc_final: 0.7702 (p0) REVERT: A 386 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7798 (mtpp) REVERT: A 420 ASP cc_start: 0.7617 (p0) cc_final: 0.7040 (t70) REVERT: A 448 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: A 509 ASP cc_start: 0.6903 (t0) cc_final: 0.6664 (t0) REVERT: A 602 ASP cc_start: 0.7505 (m-30) cc_final: 0.7270 (m-30) REVERT: A 614 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7743 (ptmt) REVERT: A 620 PHE cc_start: 0.8019 (m-80) cc_final: 0.7622 (m-10) REVERT: A 622 PHE cc_start: 0.8201 (p90) cc_final: 0.7979 (p90) REVERT: A 730 GLU cc_start: 0.6503 (tt0) cc_final: 0.6190 (tt0) REVERT: A 750 VAL cc_start: 0.8149 (t) cc_final: 0.7879 (p) REVERT: A 768 GLN cc_start: 0.7864 (mt0) cc_final: 0.7411 (mt0) REVERT: A 788 PHE cc_start: 0.7632 (m-80) cc_final: 0.7228 (m-80) REVERT: A 795 GLU cc_start: 0.7739 (tt0) cc_final: 0.7490 (tm-30) REVERT: A 820 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7494 (mttt) REVERT: A 872 TYR cc_start: 0.8382 (m-80) cc_final: 0.8182 (m-80) REVERT: A 945 VAL cc_start: 0.8439 (p) cc_final: 0.8148 (t) REVERT: A 952 MET cc_start: 0.7506 (mtm) cc_final: 0.7072 (mtm) REVERT: A 954 SER cc_start: 0.8530 (m) cc_final: 0.8217 (p) REVERT: A 1064 SER cc_start: 0.8038 (t) cc_final: 0.7625 (m) REVERT: A 1074 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7808 (mm) REVERT: A 1104 LYS cc_start: 0.8373 (mmpt) cc_final: 0.7917 (tppp) REVERT: A 1109 GLN cc_start: 0.7803 (tt0) cc_final: 0.7492 (tt0) REVERT: A 1164 VAL cc_start: 0.8276 (t) cc_final: 0.8056 (m) REVERT: A 1184 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 1213 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7319 (ptt-90) REVERT: B 217 VAL cc_start: 0.8437 (t) cc_final: 0.8182 (t) REVERT: B 219 SER cc_start: 0.8569 (t) cc_final: 0.8261 (p) REVERT: B 264 ASN cc_start: 0.6646 (OUTLIER) cc_final: 0.5986 (t0) REVERT: B 386 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8231 (mtpt) REVERT: B 420 ASP cc_start: 0.7760 (p0) cc_final: 0.7063 (t0) REVERT: B 506 SER cc_start: 0.8668 (t) cc_final: 0.8373 (m) REVERT: B 509 ASP cc_start: 0.7465 (t0) cc_final: 0.7142 (t0) REVERT: B 545 ASP cc_start: 0.7878 (p0) cc_final: 0.7454 (p0) REVERT: B 640 ASP cc_start: 0.7416 (t0) cc_final: 0.6859 (t0) REVERT: B 651 LYS cc_start: 0.8035 (tttt) cc_final: 0.7771 (ttpp) REVERT: B 682 GLN cc_start: 0.6660 (mp10) cc_final: 0.5948 (mp10) REVERT: B 704 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6260 (mt-10) REVERT: B 736 TYR cc_start: 0.8159 (t80) cc_final: 0.7913 (t80) REVERT: B 750 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7862 (p) REVERT: B 768 GLN cc_start: 0.7981 (mt0) cc_final: 0.7505 (mt0) REVERT: B 777 MET cc_start: 0.7212 (mmm) cc_final: 0.6949 (mmm) REVERT: B 814 ASN cc_start: 0.8855 (t0) cc_final: 0.8211 (t0) REVERT: B 820 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7792 (mtpp) REVERT: B 847 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: B 850 SER cc_start: 0.8582 (t) cc_final: 0.8298 (p) REVERT: B 944 VAL cc_start: 0.8747 (m) cc_final: 0.8439 (p) REVERT: B 1005 SER cc_start: 0.8321 (m) cc_final: 0.8060 (m) REVERT: B 1051 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6786 (mm-40) REVERT: B 1052 LEU cc_start: 0.8347 (tp) cc_final: 0.8007 (tp) REVERT: B 1061 GLN cc_start: 0.7760 (mp10) cc_final: 0.7522 (mm-40) REVERT: B 1084 ASP cc_start: 0.7623 (t70) cc_final: 0.7310 (t0) REVERT: B 1099 SER cc_start: 0.8467 (m) cc_final: 0.8204 (t) REVERT: B 1104 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7942 (ttmm) REVERT: B 1120 ASN cc_start: 0.8095 (m-40) cc_final: 0.7881 (m-40) REVERT: B 1218 SER cc_start: 0.8270 (m) cc_final: 0.7627 (p) REVERT: C 38 LYS cc_start: 0.7689 (ptpt) cc_final: 0.7183 (ptpt) REVERT: C 247 ASN cc_start: 0.8168 (p0) cc_final: 0.7826 (p0) REVERT: C 258 ASN cc_start: 0.6444 (m-40) cc_final: 0.5725 (m-40) REVERT: C 266 SER cc_start: 0.7921 (m) cc_final: 0.7663 (p) REVERT: C 303 ILE cc_start: 0.8261 (mm) cc_final: 0.8008 (tt) REVERT: C 346 SER cc_start: 0.8573 (m) cc_final: 0.8362 (t) REVERT: C 348 VAL cc_start: 0.7526 (OUTLIER) cc_final: 0.7227 (p) REVERT: C 386 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7820 (mttm) REVERT: C 397 GLU cc_start: 0.6383 (tt0) cc_final: 0.6096 (tt0) REVERT: C 450 LEU cc_start: 0.8005 (tp) cc_final: 0.7753 (tp) REVERT: C 462 LEU cc_start: 0.8176 (tp) cc_final: 0.7896 (tt) REVERT: C 470 GLN cc_start: 0.7448 (tp40) cc_final: 0.7144 (tp40) REVERT: C 472 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7769 (mttt) REVERT: C 506 SER cc_start: 0.8325 (t) cc_final: 0.7852 (p) REVERT: C 594 LEU cc_start: 0.7643 (tp) cc_final: 0.7247 (tp) REVERT: C 687 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8444 (ttmt) REVERT: C 691 SER cc_start: 0.8670 (p) cc_final: 0.8315 (t) REVERT: C 704 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6437 (mt-10) REVERT: C 719 SER cc_start: 0.8262 (p) cc_final: 0.7855 (t) REVERT: C 748 VAL cc_start: 0.8985 (t) cc_final: 0.8663 (p) REVERT: C 765 VAL cc_start: 0.8453 (t) cc_final: 0.8194 (m) REVERT: C 788 PHE cc_start: 0.8107 (m-80) cc_final: 0.7455 (m-80) REVERT: C 796 TYR cc_start: 0.7450 (t80) cc_final: 0.7121 (t80) REVERT: C 805 SER cc_start: 0.8210 (t) cc_final: 0.7567 (p) REVERT: C 821 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7205 (mm-40) REVERT: C 847 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7249 (tt0) REVERT: C 900 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 918 LYS cc_start: 0.8932 (mtmt) cc_final: 0.8554 (mtmt) REVERT: C 1064 SER cc_start: 0.7961 (t) cc_final: 0.7430 (m) REVERT: C 1084 ASP cc_start: 0.7300 (t70) cc_final: 0.7049 (t0) REVERT: C 1164 VAL cc_start: 0.8491 (t) cc_final: 0.8198 (m) REVERT: C 1208 ARG cc_start: 0.6140 (mtp180) cc_final: 0.5823 (ttm170) outliers start: 96 outliers final: 62 residues processed: 623 average time/residue: 0.1441 time to fit residues: 143.4419 Evaluate side-chains 635 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 564 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 918 LYS Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1213 ARG Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1113 LYS Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 92 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 868 ASN ** C 933 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 = 0.3480 r_free = 0.3480 target = 0.119587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101770 restraints weight = 38056.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105173 restraints weight = 19171.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107380 restraints weight = 11442.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108720 restraints weight = 7819.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109742 restraints weight = 6026.309| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23826 Z= 0.183 Angle : 0.637 9.889 32508 Z= 0.318 Chirality : 0.045 0.202 3933 Planarity : 0.004 0.059 4044 Dihedral : 6.053 54.044 4164 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.76 % Allowed : 17.02 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 2844 helix: 1.36 (0.21), residues: 648 sheet: -0.58 (0.20), residues: 666 loop : -1.11 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 314 TYR 0.023 0.002 TYR B 676 PHE 0.019 0.002 PHE A1141 TRP 0.007 0.001 TRP A 439 HIS 0.005 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (23736) covalent geometry : angle 0.60505 / 0.31 (32277) SS BOND : bond 0.00515 / 0.29 ( 39) SS BOND : angle 2.81782 / 1.84 ( 78) hydrogen bonds : bond 0.04265 / 2.75 ( 818) hydrogen bonds : angle 5.32127 / 3.60 ( 2400) link_ALPHA1-3 : bond 0.00998 / 0.50 ( 3) link_ALPHA1-3 : angle 1.12597 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00988 / 0.49 ( 3) link_ALPHA1-6 : angle 1.21215 / 0.92 ( 9) link_BETA1-4 : bond 0.00392 / 0.23 ( 12) link_BETA1-4 : angle 1.68570 / 1.24 ( 36) link_NAG-ASN : bond 0.00684 / 0.43 ( 33) link_NAG-ASN : angle 2.49574 / 1.70 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 576 time to evaluate : 0.756 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: A 212 TYR cc_start: 0.7592 (m-80) cc_final: 0.7273 (m-10) REVERT: A 228 GLN cc_start: 0.7127 (tm-30) cc_final: 0.6873 (tm-30) REVERT: A 245 GLU cc_start: 0.7406 (tp30) cc_final: 0.7002 (mp0) REVERT: A 247 ASN cc_start: 0.7988 (p0) cc_final: 0.7730 (p0) REVERT: A 386 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7807 (mtpp) REVERT: A 420 ASP cc_start: 0.7659 (p0) cc_final: 0.7044 (t70) REVERT: A 448 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: A 472 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7955 (mttt) REVERT: A 509 ASP cc_start: 0.6903 (t0) cc_final: 0.6668 (t0) REVERT: A 602 ASP cc_start: 0.7514 (m-30) cc_final: 0.7281 (m-30) REVERT: A 614 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7738 (ptmt) REVERT: A 620 PHE cc_start: 0.8024 (m-80) cc_final: 0.7643 (m-10) REVERT: A 705 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7837 (mm110) REVERT: A 750 VAL cc_start: 0.8238 (t) cc_final: 0.7893 (p) REVERT: A 788 PHE cc_start: 0.7664 (m-80) cc_final: 0.7431 (m-80) REVERT: A 820 LYS cc_start: 0.7847 (mtmt) cc_final: 0.7506 (mttt) REVERT: A 945 VAL cc_start: 0.8448 (p) cc_final: 0.8144 (t) REVERT: A 952 MET cc_start: 0.7451 (mtm) cc_final: 0.6937 (mtm) REVERT: A 954 SER cc_start: 0.8531 (m) cc_final: 0.8210 (p) REVERT: A 1064 SER cc_start: 0.8053 (t) cc_final: 0.7667 (m) REVERT: A 1074 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7787 (mm) REVERT: A 1104 LYS cc_start: 0.8348 (mmpt) cc_final: 0.7932 (tppp) REVERT: A 1109 GLN cc_start: 0.7812 (tt0) cc_final: 0.7548 (tt0) REVERT: A 1139 HIS cc_start: 0.6753 (t-90) cc_final: 0.6522 (t70) REVERT: A 1164 VAL cc_start: 0.8274 (t) cc_final: 0.8038 (m) REVERT: A 1184 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 1209 MET cc_start: 0.6222 (mmm) cc_final: 0.5932 (mmm) REVERT: A 1213 ARG cc_start: 0.7837 (ptt180) cc_final: 0.7378 (ptt-90) REVERT: A 1219 ASP cc_start: 0.8146 (m-30) cc_final: 0.7478 (p0) REVERT: B 217 VAL cc_start: 0.8436 (t) cc_final: 0.8191 (t) REVERT: B 219 SER cc_start: 0.8582 (t) cc_final: 0.8176 (p) REVERT: B 264 ASN cc_start: 0.6553 (OUTLIER) cc_final: 0.5969 (t0) REVERT: B 285 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7486 (mp) REVERT: B 314 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7667 (ttp-110) REVERT: B 386 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8324 (mtpt) REVERT: B 420 ASP cc_start: 0.7795 (p0) cc_final: 0.7069 (t0) REVERT: B 487 ILE cc_start: 0.8191 (pt) cc_final: 0.7861 (mt) REVERT: B 506 SER cc_start: 0.8679 (t) cc_final: 0.8391 (m) REVERT: B 509 ASP cc_start: 0.7480 (t0) cc_final: 0.7164 (t0) REVERT: B 545 ASP cc_start: 0.7844 (p0) cc_final: 0.7410 (p0) REVERT: B 551 ILE cc_start: 0.8381 (mt) cc_final: 0.8020 (tt) REVERT: B 640 ASP cc_start: 0.7416 (t0) cc_final: 0.6813 (t0) REVERT: B 651 LYS cc_start: 0.8041 (tttt) cc_final: 0.7784 (ttpp) REVERT: B 704 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6304 (mt-10) REVERT: B 730 GLU cc_start: 0.7222 (tp30) cc_final: 0.6954 (tp30) REVERT: B 750 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7898 (p) REVERT: B 768 GLN cc_start: 0.8003 (mt0) cc_final: 0.7521 (mt0) REVERT: B 814 ASN cc_start: 0.8899 (t0) cc_final: 0.8274 (t0) REVERT: B 820 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7784 (mtpp) REVERT: B 847 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: B 850 SER cc_start: 0.8595 (t) cc_final: 0.8294 (p) REVERT: B 944 VAL cc_start: 0.8792 (m) cc_final: 0.8536 (p) REVERT: B 1005 SER cc_start: 0.8338 (m) cc_final: 0.8089 (m) REVERT: B 1051 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6780 (mm-40) REVERT: B 1052 LEU cc_start: 0.8334 (tp) cc_final: 0.7998 (tp) REVERT: B 1061 GLN cc_start: 0.7749 (mp10) cc_final: 0.7495 (mm-40) REVERT: B 1084 ASP cc_start: 0.7648 (t70) cc_final: 0.7348 (t0) REVERT: B 1099 SER cc_start: 0.8483 (m) cc_final: 0.8217 (t) REVERT: B 1104 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7963 (ttmm) REVERT: B 1120 ASN cc_start: 0.8118 (m-40) cc_final: 0.7844 (m-40) REVERT: B 1218 SER cc_start: 0.8285 (m) cc_final: 0.7646 (p) REVERT: C 38 LYS cc_start: 0.7660 (ptpt) cc_final: 0.7158 (ptpt) REVERT: C 247 ASN cc_start: 0.8177 (p0) cc_final: 0.7856 (p0) REVERT: C 258 ASN cc_start: 0.6446 (m-40) cc_final: 0.5660 (m-40) REVERT: C 266 SER cc_start: 0.7963 (m) cc_final: 0.7730 (p) REVERT: C 303 ILE cc_start: 0.8289 (mm) cc_final: 0.8040 (tt) REVERT: C 348 VAL cc_start: 0.7694 (OUTLIER) cc_final: 0.7401 (p) REVERT: C 376 LYS cc_start: 0.7251 (mtpt) cc_final: 0.7028 (mtpt) REVERT: C 386 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7872 (mtpp) REVERT: C 397 GLU cc_start: 0.6387 (tt0) cc_final: 0.6082 (tt0) REVERT: C 450 LEU cc_start: 0.8033 (tp) cc_final: 0.7789 (tp) REVERT: C 462 LEU cc_start: 0.8223 (tp) cc_final: 0.7947 (tt) REVERT: C 470 GLN cc_start: 0.7391 (tp40) cc_final: 0.7106 (tp40) REVERT: C 472 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7793 (mttt) REVERT: C 506 SER cc_start: 0.8254 (t) cc_final: 0.7924 (p) REVERT: C 594 LEU cc_start: 0.7689 (tp) cc_final: 0.7294 (tp) REVERT: C 691 SER cc_start: 0.8680 (p) cc_final: 0.8279 (t) REVERT: C 704 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6431 (mt-10) REVERT: C 719 SER cc_start: 0.8293 (p) cc_final: 0.7832 (t) REVERT: C 748 VAL cc_start: 0.8996 (t) cc_final: 0.8715 (p) REVERT: C 765 VAL cc_start: 0.8524 (t) cc_final: 0.8278 (m) REVERT: C 788 PHE cc_start: 0.8154 (m-80) cc_final: 0.7496 (m-80) REVERT: C 796 TYR cc_start: 0.7444 (t80) cc_final: 0.7125 (t80) REVERT: C 805 SER cc_start: 0.8178 (t) cc_final: 0.7535 (p) REVERT: C 821 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7218 (mm-40) REVERT: C 847 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: C 900 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (tt) REVERT: C 918 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8543 (mtmt) REVERT: C 1064 SER cc_start: 0.7976 (t) cc_final: 0.7415 (m) REVERT: C 1084 ASP cc_start: 0.7339 (t70) cc_final: 0.7105 (t0) REVERT: C 1164 VAL cc_start: 0.8454 (t) cc_final: 0.8162 (m) REVERT: C 1208 ARG cc_start: 0.6209 (mtp180) cc_final: 0.5853 (ttm170) REVERT: C 1213 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7018 (ptt90) outliers start: 96 outliers final: 69 residues processed: 617 average time/residue: 0.1434 time to fit residues: 141.5723 Evaluate side-chains 627 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 548 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 958 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 237 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.098732 restraints weight = 39077.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102128 restraints weight = 19235.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104329 restraints weight = 11248.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105627 restraints weight = 7526.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106634 restraints weight = 5737.542| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23826 Z= 0.139 Angle : 0.611 9.593 32508 Z= 0.304 Chirality : 0.044 0.202 3933 Planarity : 0.004 0.058 4044 Dihedral : 5.931 54.421 4164 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.90 % Allowed : 18.51 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.15), residues: 2844 helix: 1.35 (0.21), residues: 657 sheet: -0.49 (0.21), residues: 654 loop : -1.10 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.020 0.001 TYR B 676 PHE 0.023 0.001 PHE A 622 TRP 0.010 0.001 TRP B 439 HIS 0.004 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (23736) covalent geometry : angle 0.58250 / 0.30 (32277) SS BOND : bond 0.00508 / 0.29 ( 39) SS BOND : angle 2.46008 / 1.61 ( 78) hydrogen bonds : bond 0.03952 / 2.54 ( 818) hydrogen bonds : angle 5.19133 / 3.51 ( 2400) link_ALPHA1-3 : bond 0.01027 / 0.51 ( 3) link_ALPHA1-3 : angle 1.11737 / 0.82 ( 9) link_ALPHA1-6 : bond 0.01016 / 0.51 ( 3) link_ALPHA1-6 : angle 1.25751 / 0.94 ( 9) link_BETA1-4 : bond 0.00403 / 0.23 ( 12) link_BETA1-4 : angle 1.62909 / 1.20 ( 36) link_NAG-ASN : bond 0.00554 / 0.34 ( 33) link_NAG-ASN : angle 2.44282 / 1.68 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 561 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 TYR cc_start: 0.7548 (m-80) cc_final: 0.7248 (m-10) REVERT: A 228 GLN cc_start: 0.7100 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 245 GLU cc_start: 0.7342 (tp30) cc_final: 0.6976 (mp0) REVERT: A 247 ASN cc_start: 0.7985 (p0) cc_final: 0.7740 (p0) REVERT: A 386 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7796 (mtpp) REVERT: A 396 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7456 (mtp85) REVERT: A 448 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: A 472 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7958 (mttt) REVERT: A 509 ASP cc_start: 0.6876 (t0) cc_final: 0.6636 (t0) REVERT: A 602 ASP cc_start: 0.7483 (m-30) cc_final: 0.7262 (m-30) REVERT: A 604 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7252 (pp) REVERT: A 614 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7730 (ptmt) REVERT: A 620 PHE cc_start: 0.8003 (m-80) cc_final: 0.7668 (m-10) REVERT: A 750 VAL cc_start: 0.8177 (t) cc_final: 0.7839 (p) REVERT: A 778 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7431 (p) REVERT: A 788 PHE cc_start: 0.7718 (m-80) cc_final: 0.7483 (m-80) REVERT: A 820 LYS cc_start: 0.7854 (mtmt) cc_final: 0.7476 (mttt) REVERT: A 844 GLU cc_start: 0.7475 (tt0) cc_final: 0.7232 (tt0) REVERT: A 945 VAL cc_start: 0.8410 (p) cc_final: 0.8139 (t) REVERT: A 952 MET cc_start: 0.7437 (mtm) cc_final: 0.6900 (mtm) REVERT: A 954 SER cc_start: 0.8511 (m) cc_final: 0.8117 (p) REVERT: A 1064 SER cc_start: 0.7993 (t) cc_final: 0.7596 (m) REVERT: A 1104 LYS cc_start: 0.8344 (mmpt) cc_final: 0.7900 (tppp) REVERT: A 1138 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6767 (mm-30) REVERT: A 1164 VAL cc_start: 0.8260 (t) cc_final: 0.8037 (m) REVERT: A 1184 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7109 (mm-30) REVERT: A 1209 MET cc_start: 0.6197 (mmm) cc_final: 0.5810 (mmm) REVERT: A 1213 ARG cc_start: 0.7792 (ptt180) cc_final: 0.7351 (ptt-90) REVERT: A 1219 ASP cc_start: 0.8154 (m-30) cc_final: 0.7499 (p0) REVERT: B 217 VAL cc_start: 0.8455 (t) cc_final: 0.8228 (t) REVERT: B 219 SER cc_start: 0.8566 (t) cc_final: 0.8152 (p) REVERT: B 235 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (tp) REVERT: B 264 ASN cc_start: 0.6404 (OUTLIER) cc_final: 0.5958 (t0) REVERT: B 314 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7643 (ttp-110) REVERT: B 386 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8117 (mtpp) REVERT: B 420 ASP cc_start: 0.7780 (p0) cc_final: 0.7019 (t0) REVERT: B 487 ILE cc_start: 0.8152 (pt) cc_final: 0.7845 (mt) REVERT: B 506 SER cc_start: 0.8656 (t) cc_final: 0.8380 (m) REVERT: B 509 ASP cc_start: 0.7379 (t0) cc_final: 0.7148 (t0) REVERT: B 542 PHE cc_start: 0.7395 (t80) cc_final: 0.7007 (t80) REVERT: B 545 ASP cc_start: 0.7784 (p0) cc_final: 0.7333 (p0) REVERT: B 551 ILE cc_start: 0.8364 (mt) cc_final: 0.8040 (tt) REVERT: B 602 ASP cc_start: 0.7248 (m-30) cc_final: 0.6880 (m-30) REVERT: B 640 ASP cc_start: 0.7398 (t0) cc_final: 0.6808 (t0) REVERT: B 651 LYS cc_start: 0.8034 (tttt) cc_final: 0.7798 (ttpp) REVERT: B 704 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6202 (mt-10) REVERT: B 750 VAL cc_start: 0.8161 (t) cc_final: 0.7852 (p) REVERT: B 768 GLN cc_start: 0.7990 (mt0) cc_final: 0.7522 (mt0) REVERT: B 788 PHE cc_start: 0.7975 (m-80) cc_final: 0.6740 (m-80) REVERT: B 814 ASN cc_start: 0.8857 (t0) cc_final: 0.8226 (t0) REVERT: B 820 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7688 (ttmt) REVERT: B 847 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: B 850 SER cc_start: 0.8588 (t) cc_final: 0.8285 (p) REVERT: B 944 VAL cc_start: 0.8727 (m) cc_final: 0.8454 (p) REVERT: B 954 SER cc_start: 0.8312 (m) cc_final: 0.7811 (p) REVERT: B 1005 SER cc_start: 0.8310 (m) cc_final: 0.8061 (m) REVERT: B 1052 LEU cc_start: 0.8339 (tp) cc_final: 0.7990 (tp) REVERT: B 1061 GLN cc_start: 0.7732 (mp10) cc_final: 0.7495 (mm-40) REVERT: B 1084 ASP cc_start: 0.7620 (t70) cc_final: 0.7336 (t0) REVERT: B 1099 SER cc_start: 0.8465 (m) cc_final: 0.8254 (t) REVERT: B 1104 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7942 (ttmm) REVERT: B 1120 ASN cc_start: 0.8109 (m-40) cc_final: 0.7840 (m-40) REVERT: B 1218 SER cc_start: 0.8375 (m) cc_final: 0.7751 (p) REVERT: C 38 LYS cc_start: 0.7729 (ptpt) cc_final: 0.7196 (ptpt) REVERT: C 258 ASN cc_start: 0.6516 (m-40) cc_final: 0.5425 (m-40) REVERT: C 266 SER cc_start: 0.7946 (m) cc_final: 0.7703 (p) REVERT: C 303 ILE cc_start: 0.8301 (mm) cc_final: 0.8037 (tt) REVERT: C 314 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7995 (ttp-110) REVERT: C 348 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7364 (p) REVERT: C 386 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7864 (mttm) REVERT: C 397 GLU cc_start: 0.6384 (tt0) cc_final: 0.6097 (tt0) REVERT: C 450 LEU cc_start: 0.8001 (tp) cc_final: 0.7768 (tp) REVERT: C 462 LEU cc_start: 0.8175 (tp) cc_final: 0.7912 (tt) REVERT: C 470 GLN cc_start: 0.7444 (tp40) cc_final: 0.7172 (tp40) REVERT: C 506 SER cc_start: 0.8277 (t) cc_final: 0.7863 (p) REVERT: C 594 LEU cc_start: 0.7728 (tp) cc_final: 0.7356 (tp) REVERT: C 651 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7499 (ttpp) REVERT: C 691 SER cc_start: 0.8662 (p) cc_final: 0.8258 (t) REVERT: C 704 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6407 (mt-10) REVERT: C 719 SER cc_start: 0.8214 (p) cc_final: 0.7936 (t) REVERT: C 748 VAL cc_start: 0.8990 (t) cc_final: 0.8697 (p) REVERT: C 765 VAL cc_start: 0.8524 (t) cc_final: 0.8271 (m) REVERT: C 788 PHE cc_start: 0.8141 (m-80) cc_final: 0.7546 (m-80) REVERT: C 796 TYR cc_start: 0.7443 (t80) cc_final: 0.7147 (t80) REVERT: C 805 SER cc_start: 0.8155 (t) cc_final: 0.7445 (p) REVERT: C 847 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: C 900 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8066 (tt) REVERT: C 918 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8479 (mtmt) REVERT: C 948 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6965 (tp30) REVERT: C 1064 SER cc_start: 0.7915 (t) cc_final: 0.7383 (m) REVERT: C 1084 ASP cc_start: 0.7284 (t70) cc_final: 0.7059 (t0) REVERT: C 1104 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7915 (tppp) REVERT: C 1164 VAL cc_start: 0.8464 (t) cc_final: 0.8175 (m) REVERT: C 1208 ARG cc_start: 0.6196 (mtp180) cc_final: 0.5871 (ttm170) REVERT: C 1214 LYS cc_start: 0.8563 (mmpt) cc_final: 0.8280 (mmmt) outliers start: 74 outliers final: 60 residues processed: 600 average time/residue: 0.1421 time to fit residues: 137.4084 Evaluate side-chains 625 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 556 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 141 optimal weight: 2.9990 chunk 140 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095943 restraints weight = 39299.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099245 restraints weight = 19461.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101390 restraints weight = 11505.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.102800 restraints weight = 7755.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103724 restraints weight = 5849.851| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23826 Z= 0.215 Angle : 0.677 11.192 32508 Z= 0.337 Chirality : 0.046 0.188 3933 Planarity : 0.004 0.060 4044 Dihedral : 6.183 54.106 4164 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.49 % Allowed : 18.20 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.70 (0.15), residues: 2844 helix: 1.18 (0.21), residues: 657 sheet: -0.50 (0.21), residues: 648 loop : -1.18 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 314 TYR 0.022 0.002 TYR B 676 PHE 0.022 0.002 PHE B 788 TRP 0.013 0.001 TRP B 439 HIS 0.005 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (23736) covalent geometry : angle 0.64722 / 0.33 (32277) SS BOND : bond 0.00549 / 0.31 ( 39) SS BOND : angle 2.73848 / 1.87 ( 78) hydrogen bonds : bond 0.04413 / 2.84 ( 818) hydrogen bonds : angle 5.31137 / 3.60 ( 2400) link_ALPHA1-3 : bond 0.01118 / 0.56 ( 3) link_ALPHA1-3 : angle 1.27038 / 0.86 ( 9) link_ALPHA1-6 : bond 0.01035 / 0.51 ( 3) link_ALPHA1-6 : angle 1.21721 / 0.93 ( 9) link_BETA1-4 : bond 0.00398 / 0.25 ( 12) link_BETA1-4 : angle 1.70505 / 1.27 ( 36) link_NAG-ASN : bond 0.00621 / 0.37 ( 33) link_NAG-ASN : angle 2.57340 / 1.78 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 573 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASN cc_start: 0.7863 (m-40) cc_final: 0.7478 (m-40) REVERT: A 228 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6681 (tm-30) REVERT: A 247 ASN cc_start: 0.8023 (p0) cc_final: 0.7779 (p0) REVERT: A 280 LEU cc_start: 0.8313 (tp) cc_final: 0.8030 (tt) REVERT: A 386 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7771 (mtpp) REVERT: A 393 PRO cc_start: 0.8004 (Cg_endo) cc_final: 0.7772 (Cg_exo) REVERT: A 396 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7116 (mtp85) REVERT: A 420 ASP cc_start: 0.7611 (p0) cc_final: 0.7068 (t70) REVERT: A 448 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: A 472 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7825 (mttt) REVERT: A 509 ASP cc_start: 0.7017 (t0) cc_final: 0.6548 (t0) REVERT: A 614 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7723 (ptmt) REVERT: A 620 PHE cc_start: 0.8027 (m-80) cc_final: 0.7780 (m-10) REVERT: A 750 VAL cc_start: 0.8338 (t) cc_final: 0.8008 (p) REVERT: A 778 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7619 (p) REVERT: A 789 SER cc_start: 0.8055 (p) cc_final: 0.7855 (p) REVERT: A 820 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7593 (mttt) REVERT: A 844 GLU cc_start: 0.7598 (tt0) cc_final: 0.7337 (tt0) REVERT: A 895 SER cc_start: 0.8498 (p) cc_final: 0.8113 (t) REVERT: A 945 VAL cc_start: 0.8523 (p) cc_final: 0.8258 (t) REVERT: A 952 MET cc_start: 0.7633 (mtm) cc_final: 0.7031 (mtm) REVERT: A 954 SER cc_start: 0.8357 (m) cc_final: 0.8052 (p) REVERT: A 1064 SER cc_start: 0.8164 (t) cc_final: 0.7768 (m) REVERT: A 1104 LYS cc_start: 0.8358 (mmpt) cc_final: 0.7908 (tppp) REVERT: A 1109 GLN cc_start: 0.7831 (tt0) cc_final: 0.7618 (tt0) REVERT: A 1164 VAL cc_start: 0.8197 (t) cc_final: 0.7951 (m) REVERT: A 1184 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 1209 MET cc_start: 0.6203 (mmm) cc_final: 0.5832 (mmm) REVERT: A 1213 ARG cc_start: 0.7802 (ptt180) cc_final: 0.7335 (ptt-90) REVERT: A 1219 ASP cc_start: 0.8258 (m-30) cc_final: 0.7505 (p0) REVERT: B 217 VAL cc_start: 0.8380 (t) cc_final: 0.8155 (t) REVERT: B 219 SER cc_start: 0.8612 (t) cc_final: 0.8217 (p) REVERT: B 235 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8637 (tp) REVERT: B 264 ASN cc_start: 0.6399 (OUTLIER) cc_final: 0.6015 (t0) REVERT: B 314 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7519 (ttp-110) REVERT: B 386 LYS cc_start: 0.8611 (mtpt) cc_final: 0.7997 (mtpp) REVERT: B 420 ASP cc_start: 0.7815 (p0) cc_final: 0.7078 (t0) REVERT: B 487 ILE cc_start: 0.8001 (pt) cc_final: 0.7799 (mt) REVERT: B 506 SER cc_start: 0.8723 (t) cc_final: 0.8354 (m) REVERT: B 509 ASP cc_start: 0.7530 (t0) cc_final: 0.7232 (t0) REVERT: B 545 ASP cc_start: 0.7896 (p0) cc_final: 0.7462 (p0) REVERT: B 551 ILE cc_start: 0.8336 (mt) cc_final: 0.8000 (tt) REVERT: B 651 LYS cc_start: 0.8009 (tttt) cc_final: 0.7751 (ttpp) REVERT: B 704 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6224 (mt-10) REVERT: B 750 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.7993 (p) REVERT: B 768 GLN cc_start: 0.8067 (mt0) cc_final: 0.7575 (mt0) REVERT: B 814 ASN cc_start: 0.8938 (t0) cc_final: 0.8310 (t0) REVERT: B 820 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7699 (ttmt) REVERT: B 847 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: B 850 SER cc_start: 0.8680 (t) cc_final: 0.8242 (p) REVERT: B 944 VAL cc_start: 0.8861 (m) cc_final: 0.8619 (p) REVERT: B 1005 SER cc_start: 0.8315 (m) cc_final: 0.8070 (m) REVERT: B 1051 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6842 (mm-40) REVERT: B 1052 LEU cc_start: 0.8261 (tp) cc_final: 0.7941 (tp) REVERT: B 1061 GLN cc_start: 0.7879 (mp10) cc_final: 0.7621 (mm-40) REVERT: B 1084 ASP cc_start: 0.7738 (t70) cc_final: 0.7447 (t0) REVERT: B 1099 SER cc_start: 0.8385 (m) cc_final: 0.8156 (t) REVERT: B 1104 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7919 (ttmm) REVERT: B 1120 ASN cc_start: 0.8175 (m-40) cc_final: 0.7825 (m-40) REVERT: B 1209 MET cc_start: 0.5655 (mmm) cc_final: 0.5315 (mmm) REVERT: B 1218 SER cc_start: 0.8530 (m) cc_final: 0.7862 (p) REVERT: C 38 LYS cc_start: 0.8004 (ptpt) cc_final: 0.7485 (ptpt) REVERT: C 266 SER cc_start: 0.8171 (m) cc_final: 0.7928 (p) REVERT: C 303 ILE cc_start: 0.8384 (mm) cc_final: 0.8088 (tt) REVERT: C 348 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7334 (p) REVERT: C 386 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7835 (mttm) REVERT: C 450 LEU cc_start: 0.8058 (tp) cc_final: 0.7826 (tp) REVERT: C 462 LEU cc_start: 0.8271 (tp) cc_final: 0.8012 (tt) REVERT: C 470 GLN cc_start: 0.7522 (tp40) cc_final: 0.7234 (tp40) REVERT: C 472 LYS cc_start: 0.7929 (mtpt) cc_final: 0.7670 (mttt) REVERT: C 506 SER cc_start: 0.8119 (t) cc_final: 0.7757 (p) REVERT: C 594 LEU cc_start: 0.7879 (tp) cc_final: 0.7543 (tp) REVERT: C 691 SER cc_start: 0.8748 (p) cc_final: 0.8354 (t) REVERT: C 704 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6520 (mt-10) REVERT: C 719 SER cc_start: 0.8360 (p) cc_final: 0.7944 (t) REVERT: C 748 VAL cc_start: 0.9009 (t) cc_final: 0.8727 (p) REVERT: C 758 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7774 (ttmm) REVERT: C 765 VAL cc_start: 0.8521 (t) cc_final: 0.8276 (m) REVERT: C 788 PHE cc_start: 0.8189 (m-80) cc_final: 0.7444 (m-80) REVERT: C 796 TYR cc_start: 0.7577 (t80) cc_final: 0.7194 (t80) REVERT: C 805 SER cc_start: 0.8128 (t) cc_final: 0.7422 (p) REVERT: C 847 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: C 900 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8054 (tt) REVERT: C 918 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8474 (mtmt) REVERT: C 961 MET cc_start: 0.6485 (mtm) cc_final: 0.6167 (ptp) REVERT: C 1064 SER cc_start: 0.8082 (t) cc_final: 0.7332 (m) REVERT: C 1084 ASP cc_start: 0.7445 (t70) cc_final: 0.7184 (t0) REVERT: C 1164 VAL cc_start: 0.8358 (t) cc_final: 0.8036 (m) REVERT: C 1208 ARG cc_start: 0.6417 (mtp180) cc_final: 0.5928 (ttm170) REVERT: C 1220 PHE cc_start: 0.8682 (m-80) cc_final: 0.8135 (m-80) outliers start: 89 outliers final: 67 residues processed: 615 average time/residue: 0.1446 time to fit residues: 142.5441 Evaluate side-chains 638 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 562 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1039 GLN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 234 CYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 900 LEU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 135 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 chunk 142 optimal weight: 0.0770 chunk 45 optimal weight: 0.3980 chunk 201 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 291 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101037 restraints weight = 38728.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104418 restraints weight = 19267.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106611 restraints weight = 11357.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107881 restraints weight = 7657.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108897 restraints weight = 5886.800| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23826 Z= 0.117 Angle : 0.628 11.224 32508 Z= 0.311 Chirality : 0.044 0.190 3933 Planarity : 0.004 0.055 4044 Dihedral : 5.904 55.052 4164 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.63 % Allowed : 20.00 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.16), residues: 2844 helix: 1.60 (0.21), residues: 636 sheet: -0.53 (0.20), residues: 678 loop : -1.08 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 314 TYR 0.026 0.001 TYR C 212 PHE 0.021 0.001 PHE A 788 TRP 0.008 0.001 TRP A 439 HIS 0.004 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (23736) covalent geometry : angle 0.60277 / 0.30 (32277) SS BOND : bond 0.00414 / 0.22 ( 39) SS BOND : angle 2.29401 / 1.59 ( 78) hydrogen bonds : bond 0.03770 / 2.41 ( 818) hydrogen bonds : angle 5.06888 / 3.42 ( 2400) link_ALPHA1-3 : bond 0.01019 / 0.51 ( 3) link_ALPHA1-3 : angle 1.13422 / 0.86 ( 9) link_ALPHA1-6 : bond 0.01025 / 0.51 ( 3) link_ALPHA1-6 : angle 1.27177 / 0.95 ( 9) link_BETA1-4 : bond 0.00405 / 0.23 ( 12) link_BETA1-4 : angle 1.57879 / 1.15 ( 36) link_NAG-ASN : bond 0.00673 / 0.42 ( 33) link_NAG-ASN : angle 2.42602 / 1.69 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 560 time to evaluate : 0.849 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: A 40 ASN cc_start: 0.7667 (m-40) cc_final: 0.7297 (m-40) REVERT: A 228 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6907 (tm-30) REVERT: A 247 ASN cc_start: 0.7949 (p0) cc_final: 0.7669 (p0) REVERT: A 396 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7100 (mtp85) REVERT: A 420 ASP cc_start: 0.7623 (p0) cc_final: 0.7146 (t70) REVERT: A 448 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: A 509 ASP cc_start: 0.6988 (t0) cc_final: 0.6675 (t0) REVERT: A 614 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7693 (ptmt) REVERT: A 620 PHE cc_start: 0.8066 (m-80) cc_final: 0.7762 (m-10) REVERT: A 750 VAL cc_start: 0.8203 (t) cc_final: 0.7858 (p) REVERT: A 788 PHE cc_start: 0.7804 (m-80) cc_final: 0.7232 (m-80) REVERT: A 790 MET cc_start: 0.7495 (mtm) cc_final: 0.7118 (mtp) REVERT: A 820 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7561 (mttt) REVERT: A 844 GLU cc_start: 0.7539 (tt0) cc_final: 0.7255 (tt0) REVERT: A 945 VAL cc_start: 0.8400 (p) cc_final: 0.8112 (t) REVERT: A 954 SER cc_start: 0.8355 (m) cc_final: 0.7966 (p) REVERT: A 1064 SER cc_start: 0.8063 (t) cc_final: 0.7714 (m) REVERT: A 1104 LYS cc_start: 0.8306 (mmpt) cc_final: 0.7880 (tppp) REVERT: A 1138 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 1164 VAL cc_start: 0.8249 (t) cc_final: 0.8011 (m) REVERT: A 1213 ARG cc_start: 0.7942 (ptt180) cc_final: 0.7519 (ptt-90) REVERT: A 1219 ASP cc_start: 0.8092 (m-30) cc_final: 0.7428 (p0) REVERT: B 217 VAL cc_start: 0.8454 (t) cc_final: 0.8231 (t) REVERT: B 314 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7460 (ttp-110) REVERT: B 386 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8103 (mttp) REVERT: B 420 ASP cc_start: 0.7808 (p0) cc_final: 0.6992 (t0) REVERT: B 487 ILE cc_start: 0.8100 (pt) cc_final: 0.7861 (mt) REVERT: B 506 SER cc_start: 0.8647 (t) cc_final: 0.8380 (m) REVERT: B 545 ASP cc_start: 0.7694 (p0) cc_final: 0.7216 (p0) REVERT: B 551 ILE cc_start: 0.8324 (mt) cc_final: 0.8004 (tt) REVERT: B 577 GLN cc_start: 0.7437 (tp40) cc_final: 0.7133 (tp40) REVERT: B 602 ASP cc_start: 0.7219 (m-30) cc_final: 0.6872 (m-30) REVERT: B 640 ASP cc_start: 0.7388 (t0) cc_final: 0.6918 (t70) REVERT: B 651 LYS cc_start: 0.8017 (tttt) cc_final: 0.7762 (ttpp) REVERT: B 704 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6158 (mt-10) REVERT: B 750 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7814 (p) REVERT: B 768 GLN cc_start: 0.7995 (mt0) cc_final: 0.7528 (mt0) REVERT: B 814 ASN cc_start: 0.8867 (t0) cc_final: 0.8220 (t0) REVERT: B 820 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7737 (ttmt) REVERT: B 847 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6977 (tt0) REVERT: B 850 SER cc_start: 0.8662 (t) cc_final: 0.8364 (p) REVERT: B 899 ASP cc_start: 0.7795 (m-30) cc_final: 0.7507 (t70) REVERT: B 902 PHE cc_start: 0.8031 (m-80) cc_final: 0.7792 (m-80) REVERT: B 944 VAL cc_start: 0.8623 (m) cc_final: 0.8358 (p) REVERT: B 1005 SER cc_start: 0.8289 (m) cc_final: 0.8036 (m) REVERT: B 1052 LEU cc_start: 0.8318 (tp) cc_final: 0.7988 (tp) REVERT: B 1061 GLN cc_start: 0.7742 (mp10) cc_final: 0.7497 (mm-40) REVERT: B 1084 ASP cc_start: 0.7624 (t70) cc_final: 0.7338 (t0) REVERT: B 1104 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7944 (ttmm) REVERT: B 1120 ASN cc_start: 0.8111 (m-40) cc_final: 0.7842 (m-40) REVERT: B 1213 ARG cc_start: 0.7728 (ptm-80) cc_final: 0.7244 (ptm160) REVERT: B 1218 SER cc_start: 0.8404 (m) cc_final: 0.7756 (p) REVERT: C 38 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7306 (ptpt) REVERT: C 247 ASN cc_start: 0.8090 (p0) cc_final: 0.7876 (p0) REVERT: C 258 ASN cc_start: 0.6304 (m-40) cc_final: 0.5567 (m-40) REVERT: C 266 SER cc_start: 0.8032 (m) cc_final: 0.7773 (p) REVERT: C 303 ILE cc_start: 0.8334 (mm) cc_final: 0.8023 (tt) REVERT: C 314 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7977 (ttp-110) REVERT: C 348 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7279 (p) REVERT: C 386 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7881 (mttm) REVERT: C 397 GLU cc_start: 0.6427 (tt0) cc_final: 0.6114 (tt0) REVERT: C 450 LEU cc_start: 0.7983 (tp) cc_final: 0.7749 (tp) REVERT: C 462 LEU cc_start: 0.8193 (tp) cc_final: 0.7970 (tt) REVERT: C 470 GLN cc_start: 0.7445 (tp40) cc_final: 0.7176 (tp40) REVERT: C 472 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7779 (mttt) REVERT: C 506 SER cc_start: 0.8221 (t) cc_final: 0.7807 (p) REVERT: C 578 SER cc_start: 0.8075 (m) cc_final: 0.7772 (p) REVERT: C 594 LEU cc_start: 0.7780 (tp) cc_final: 0.7499 (tp) REVERT: C 691 SER cc_start: 0.8676 (p) cc_final: 0.8235 (t) REVERT: C 704 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6363 (mt-10) REVERT: C 748 VAL cc_start: 0.8999 (t) cc_final: 0.8702 (p) REVERT: C 765 VAL cc_start: 0.8481 (t) cc_final: 0.8225 (m) REVERT: C 788 PHE cc_start: 0.8174 (m-80) cc_final: 0.7389 (m-80) REVERT: C 796 TYR cc_start: 0.7576 (t80) cc_final: 0.7216 (t80) REVERT: C 805 SER cc_start: 0.8103 (t) cc_final: 0.7385 (p) REVERT: C 821 GLN cc_start: 0.7454 (mm-40) cc_final: 0.7085 (mm-40) REVERT: C 847 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: C 918 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8490 (mtmt) REVERT: C 1064 SER cc_start: 0.7935 (t) cc_final: 0.7291 (m) REVERT: C 1084 ASP cc_start: 0.7278 (t70) cc_final: 0.7047 (t0) REVERT: C 1164 VAL cc_start: 0.8453 (t) cc_final: 0.8166 (m) REVERT: C 1208 ARG cc_start: 0.6186 (mtp180) cc_final: 0.5839 (ttm170) REVERT: C 1220 PHE cc_start: 0.8694 (m-80) cc_final: 0.8230 (m-80) outliers start: 67 outliers final: 52 residues processed: 593 average time/residue: 0.1450 time to fit residues: 137.0047 Evaluate side-chains 608 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 551 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 920 CYS Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 0.0060 chunk 129 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 284 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 286 optimal weight: 0.0050 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 849 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098598 restraints weight = 39766.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101641 restraints weight = 20151.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103791 restraints weight = 12217.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105169 restraints weight = 8301.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105958 restraints weight = 6280.736| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23826 Z= 0.114 Angle : 0.624 10.676 32508 Z= 0.308 Chirality : 0.044 0.188 3933 Planarity : 0.004 0.055 4044 Dihedral : 5.683 54.051 4164 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.35 % Allowed : 20.55 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2844 helix: 1.66 (0.21), residues: 642 sheet: -0.54 (0.20), residues: 699 loop : -1.02 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 314 TYR 0.026 0.001 TYR B 380 PHE 0.019 0.001 PHE A 622 TRP 0.011 0.001 TRP A 439 HIS 0.003 0.000 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (23736) covalent geometry : angle 0.59778 / 0.30 (32277) SS BOND : bond 0.00411 / 0.22 ( 39) SS BOND : angle 2.26369 / 1.58 ( 78) hydrogen bonds : bond 0.03500 / 2.24 ( 818) hydrogen bonds : angle 4.90637 / 3.31 ( 2400) link_ALPHA1-3 : bond 0.01019 / 0.51 ( 3) link_ALPHA1-3 : angle 1.10766 / 0.83 ( 9) link_ALPHA1-6 : bond 0.01074 / 0.54 ( 3) link_ALPHA1-6 : angle 1.31583 / 0.98 ( 9) link_BETA1-4 : bond 0.00424 / 0.24 ( 12) link_BETA1-4 : angle 1.58352 / 1.16 ( 36) link_NAG-ASN : bond 0.00695 / 0.45 ( 33) link_NAG-ASN : angle 2.51197 / 1.78 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 561 time to evaluate : 0.905 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: A 40 ASN cc_start: 0.7702 (m-40) cc_final: 0.7365 (m-40) REVERT: A 228 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6735 (tm-30) REVERT: A 247 ASN cc_start: 0.7918 (p0) cc_final: 0.7643 (p0) REVERT: A 384 VAL cc_start: 0.8342 (p) cc_final: 0.8075 (m) REVERT: A 386 LYS cc_start: 0.8067 (mttt) cc_final: 0.7740 (ttmm) REVERT: A 396 ARG cc_start: 0.7631 (mtp85) cc_final: 0.6912 (mtp85) REVERT: A 420 ASP cc_start: 0.7628 (p0) cc_final: 0.7110 (t0) REVERT: A 448 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: A 472 LYS cc_start: 0.8047 (mtpt) cc_final: 0.7804 (mttt) REVERT: A 509 ASP cc_start: 0.7085 (t0) cc_final: 0.6577 (t0) REVERT: A 614 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7689 (ptmt) REVERT: A 620 PHE cc_start: 0.7997 (m-80) cc_final: 0.7765 (m-10) REVERT: A 750 VAL cc_start: 0.8132 (t) cc_final: 0.7774 (p) REVERT: A 765 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 790 MET cc_start: 0.7474 (mtm) cc_final: 0.7014 (mtp) REVERT: A 814 ASN cc_start: 0.8906 (t0) cc_final: 0.8360 (t0) REVERT: A 820 LYS cc_start: 0.7884 (mtmt) cc_final: 0.7536 (mttt) REVERT: A 844 GLU cc_start: 0.7657 (tt0) cc_final: 0.7405 (tt0) REVERT: A 945 VAL cc_start: 0.8388 (p) cc_final: 0.8119 (t) REVERT: A 952 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: A 954 SER cc_start: 0.8265 (m) cc_final: 0.7943 (p) REVERT: A 1064 SER cc_start: 0.8068 (t) cc_final: 0.7780 (m) REVERT: A 1069 ASP cc_start: 0.7866 (t70) cc_final: 0.7511 (t0) REVERT: A 1104 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7890 (tppp) REVERT: A 1138 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 1164 VAL cc_start: 0.8122 (t) cc_final: 0.7883 (m) REVERT: A 1219 ASP cc_start: 0.8216 (m-30) cc_final: 0.8008 (m-30) REVERT: B 217 VAL cc_start: 0.8318 (t) cc_final: 0.8075 (t) REVERT: B 314 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7630 (ttp-110) REVERT: B 317 GLU cc_start: 0.7211 (pt0) cc_final: 0.6826 (pm20) REVERT: B 386 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7864 (mttp) REVERT: B 396 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7755 (mtp85) REVERT: B 420 ASP cc_start: 0.7857 (p0) cc_final: 0.6996 (t0) REVERT: B 499 ILE cc_start: 0.8522 (mm) cc_final: 0.8235 (mm) REVERT: B 506 SER cc_start: 0.8675 (t) cc_final: 0.8313 (m) REVERT: B 545 ASP cc_start: 0.7775 (p0) cc_final: 0.7481 (p0) REVERT: B 551 ILE cc_start: 0.8225 (mt) cc_final: 0.7932 (tt) REVERT: B 577 GLN cc_start: 0.7556 (tp40) cc_final: 0.7241 (tp40) REVERT: B 602 ASP cc_start: 0.7286 (m-30) cc_final: 0.6803 (m-30) REVERT: B 640 ASP cc_start: 0.7483 (t0) cc_final: 0.7035 (t70) REVERT: B 651 LYS cc_start: 0.7910 (tttt) cc_final: 0.7632 (ttpp) REVERT: B 704 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6193 (mt-10) REVERT: B 768 GLN cc_start: 0.8086 (mt0) cc_final: 0.7543 (mt0) REVERT: B 788 PHE cc_start: 0.7534 (m-80) cc_final: 0.7275 (m-80) REVERT: B 814 ASN cc_start: 0.8820 (t0) cc_final: 0.8168 (t0) REVERT: B 820 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7816 (ttmt) REVERT: B 847 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: B 850 SER cc_start: 0.8660 (t) cc_final: 0.8280 (p) REVERT: B 954 SER cc_start: 0.8284 (m) cc_final: 0.7815 (p) REVERT: B 1005 SER cc_start: 0.8275 (m) cc_final: 0.8018 (m) REVERT: B 1052 LEU cc_start: 0.8258 (tp) cc_final: 0.7971 (tp) REVERT: B 1061 GLN cc_start: 0.7857 (mp10) cc_final: 0.7605 (mm-40) REVERT: B 1070 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 1084 ASP cc_start: 0.7724 (t70) cc_final: 0.7398 (t0) REVERT: B 1104 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7896 (ttmm) REVERT: B 1120 ASN cc_start: 0.7990 (m-40) cc_final: 0.7703 (m-40) REVERT: B 1209 MET cc_start: 0.5105 (mmm) cc_final: 0.4643 (mmp) REVERT: B 1213 ARG cc_start: 0.7619 (ptm-80) cc_final: 0.7115 (ptm160) REVERT: B 1218 SER cc_start: 0.8492 (m) cc_final: 0.8113 (p) REVERT: C 38 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7471 (ptpt) REVERT: C 258 ASN cc_start: 0.6431 (m-40) cc_final: 0.5694 (m-40) REVERT: C 266 SER cc_start: 0.7974 (m) cc_final: 0.7760 (p) REVERT: C 303 ILE cc_start: 0.8377 (mm) cc_final: 0.7955 (tt) REVERT: C 314 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7928 (ttp-110) REVERT: C 348 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7225 (p) REVERT: C 386 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7777 (mttm) REVERT: C 397 GLU cc_start: 0.6594 (tt0) cc_final: 0.6216 (tt0) REVERT: C 450 LEU cc_start: 0.7903 (tp) cc_final: 0.7696 (tp) REVERT: C 462 LEU cc_start: 0.8194 (tp) cc_final: 0.7931 (tt) REVERT: C 470 GLN cc_start: 0.7580 (tp40) cc_final: 0.7344 (tp40) REVERT: C 472 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7578 (mttt) REVERT: C 506 SER cc_start: 0.8229 (t) cc_final: 0.8019 (t) REVERT: C 568 GLN cc_start: 0.7276 (mt0) cc_final: 0.7076 (mm-40) REVERT: C 578 SER cc_start: 0.8193 (m) cc_final: 0.7684 (p) REVERT: C 594 LEU cc_start: 0.8013 (tp) cc_final: 0.7752 (tp) REVERT: C 691 SER cc_start: 0.8696 (p) cc_final: 0.8392 (t) REVERT: C 704 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6545 (mt-10) REVERT: C 748 VAL cc_start: 0.9007 (t) cc_final: 0.8664 (p) REVERT: C 765 VAL cc_start: 0.8478 (t) cc_final: 0.8256 (m) REVERT: C 788 PHE cc_start: 0.8073 (m-80) cc_final: 0.7209 (m-80) REVERT: C 796 TYR cc_start: 0.7453 (t80) cc_final: 0.7152 (t80) REVERT: C 821 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7118 (mm-40) REVERT: C 847 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: C 917 TYR cc_start: 0.8930 (m-80) cc_final: 0.8654 (m-80) REVERT: C 918 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8332 (mtmt) REVERT: C 1064 SER cc_start: 0.8006 (t) cc_final: 0.7432 (m) REVERT: C 1084 ASP cc_start: 0.7313 (t70) cc_final: 0.7067 (t0) REVERT: C 1164 VAL cc_start: 0.8306 (t) cc_final: 0.8052 (m) REVERT: C 1208 ARG cc_start: 0.6474 (mtp180) cc_final: 0.6046 (ttm170) REVERT: C 1220 PHE cc_start: 0.8508 (m-80) cc_final: 0.8144 (m-80) outliers start: 60 outliers final: 44 residues processed: 593 average time/residue: 0.1497 time to fit residues: 141.2989 Evaluate side-chains 599 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 548 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1156 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 228 GLN Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 895 SER Chi-restraints excluded: chain B residue 920 CYS Chi-restraints excluded: chain B residue 952 MET Chi-restraints excluded: chain B residue 1065 SER Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 958 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 103 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 98 optimal weight: 7.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 GLN C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095930 restraints weight = 39609.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099040 restraints weight = 20174.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101074 restraints weight = 12142.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102444 restraints weight = 8308.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103331 restraints weight = 6295.956| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23826 Z= 0.186 Angle : 0.659 10.464 32508 Z= 0.329 Chirality : 0.045 0.224 3933 Planarity : 0.004 0.058 4044 Dihedral : 5.989 54.048 4164 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.47 % Allowed : 20.82 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.58 (0.16), residues: 2844 helix: 1.36 (0.21), residues: 657 sheet: -0.51 (0.20), residues: 648 loop : -1.11 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 314 TYR 0.026 0.002 TYR B 380 PHE 0.031 0.002 PHE A 670 TRP 0.012 0.001 TRP B 439 HIS 0.005 0.001 HIS B 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (23736) covalent geometry : angle 0.63234 / 0.32 (32277) SS BOND : bond 0.00513 / 0.28 ( 39) SS BOND : angle 2.53030 / 1.73 ( 78) hydrogen bonds : bond 0.04081 / 2.62 ( 818) hydrogen bonds : angle 5.08334 / 3.44 ( 2400) link_ALPHA1-3 : bond 0.01010 / 0.50 ( 3) link_ALPHA1-3 : angle 1.17580 / 0.82 ( 9) link_ALPHA1-6 : bond 0.00974 / 0.49 ( 3) link_ALPHA1-6 : angle 1.21204 / 0.93 ( 9) link_BETA1-4 : bond 0.00403 / 0.24 ( 12) link_BETA1-4 : angle 1.65988 / 1.23 ( 36) link_NAG-ASN : bond 0.00618 / 0.38 ( 33) link_NAG-ASN : angle 2.47911 / 1.73 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.41 seconds wall clock time: 69 minutes 38.82 seconds (4178.82 seconds total)