Starting phenix.real_space_refine on Sun Sep 13 18:53:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo4_67069/09_2026/9xo4_67069.map" } resolution = 3.69 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 118 5.16 5 C 15560 2.51 5 N 3903 2.21 5 O 4854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 24435 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7493 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 37, 'TRANS': 937} Chain breaks: 18 Chain: "B" Number of atoms: 7487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 7487 Classifications: {'peptide': 975} Link IDs: {'PTRANS': 37, 'TRANS': 937} Chain breaks: 18 Chain: "C" Number of atoms: 8726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 8726 Classifications: {'peptide': 1136} Link IDs: {'PTRANS': 41, 'TRANS': 1094} Chain breaks: 9 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 4.85, per 1000 atoms: 0.20 Number of scatterers: 24435 At special positions: 0 Unit cell: (135.96, 165, 162.36, 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 118 16.00 O 4854 8.00 N 3903 7.00 C 15560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.02 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=2.02 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 26 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 202 " 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=2.04 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 J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " 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 C1401 " - " ASN C 324 " " NAG C1402 " - " ASN C 216 " " NAG C1403 " - " ASN C 514 " " NAG C1404 " - " ASN C 688 " " NAG C1405 " - " ASN C 726 " " NAG C1406 " - " ASN C 781 " " NAG C1407 " - " ASN C 743 " " NAG C1408 " - " ASN C 787 " " NAG C1409 " - " ASN C 873 " " NAG C1410 " - " ASN C1232 " " NAG C1411 " - " ASN C 344 " " NAG C1412 " - " ASN C 351 " " 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 873 " " NAG J 1 " - " ASN B 264 " " NAG K 1 " - " ASN C 264 " " NAG L 1 " - " ASN C 425 " Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 957.8 milliseconds 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 47 sheets defined 22.6% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.013A pdb=" N PHE A 39 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 40 " --> pdb=" O SER A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 233 through 238 removed outlier: 4.000A pdb=" N SER A 238 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.828A 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: 3.972A pdb=" N TYR A 811 " --> pdb=" O ASP A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.942A 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 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 922 removed outlier: 3.932A pdb=" N SER A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 917 through 922' Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 959 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.835A 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 Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.720A pdb=" N VAL A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A1084 " --> pdb=" O ASP A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'B' and resid 233 through 239 removed outlier: 3.775A pdb=" N SER B 238 " --> pdb=" O CYS B 234 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.757A 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 816 through 825 removed outlier: 3.897A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 852 removed outlier: 3.904A pdb=" N LEU B 839 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.670A pdb=" N GLN B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 861 " --> pdb=" O GLU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 917 through 922 removed outlier: 4.013A pdb=" N SER B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 917 through 922' Processing helix chain 'B' and resid 928 through 936 removed outlier: 3.513A 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 974 through 986 removed outlier: 3.559A 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: 3.557A 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: 3.546A pdb=" N LEU B1074 " --> pdb=" O ILE B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1123 removed outlier: 3.606A pdb=" N VAL B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'C' and resid 221 through 225 removed outlier: 3.503A pdb=" N GLY C 224 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C 225 " --> pdb=" O GLU C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 225' Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.574A pdb=" N VAL C 328 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 466 through 475 removed outlier: 3.670A pdb=" N GLN C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 813 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.576A pdb=" N THR C 832 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 833 " --> pdb=" O ALA C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 860 removed outlier: 3.928A pdb=" N GLN C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 917 through 921 Processing helix chain 'C' and resid 928 through 936 removed outlier: 3.517A pdb=" N SER C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.874A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 984 " --> pdb=" O ALA C 980 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU C 985 " --> pdb=" O ARG C 981 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1015 removed outlier: 3.724A pdb=" N THR C1011 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C1012 " --> pdb=" O GLY C1008 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C1013 " --> pdb=" O ASN C1009 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C1014 " --> pdb=" O MET C1010 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C1015 " --> pdb=" O THR C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1044 Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1075 through 1123 removed outlier: 3.532A pdb=" N ASP C1080 " --> pdb=" O ILE C1076 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C1081 " --> pdb=" O LEU C1077 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C1086 " --> pdb=" O GLN C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'C' and resid 1234 through 1236 No H-bonds generated for 'chain 'C' and resid 1234 through 1236' Processing helix chain 'C' and resid 1237 through 1242 removed outlier: 3.616A pdb=" N VAL C1241 " --> pdb=" O GLN C1237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.775A pdb=" N ALA A 45 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 176 removed outlier: 3.789A pdb=" N GLY A 165 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 79 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 207 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 278 removed outlier: 3.581A pdb=" N SER A 275 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 449 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 286 removed outlier: 3.524A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 318 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 298 removed outlier: 3.502A pdb=" N GLN A 295 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 421 " --> pdb=" O HIS A 338 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 344 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 348 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR A 371 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL A 390 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 388 " --> pdb=" O CYS A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 488 removed outlier: 4.007A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 718 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 738 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 727 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.589A pdb=" N GLY A 659 " --> pdb=" O TYR A 652 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 685 " --> pdb=" O TYR A 676 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 531 through 536 removed outlier: 4.106A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 550 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 517 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N PHE A 622 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 12.246A pdb=" N SER A 591 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N LYS A 624 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 11.999A pdb=" N CYS A 589 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N GLU A 626 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N LYS A 587 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 536 removed outlier: 4.106A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 550 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 517 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 549 " --> pdb=" O THR A 629 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 747 through 749 removed outlier: 6.505A pdb=" N VAL A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 780 through 798 removed outlier: 4.237A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 782 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A1154 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.237A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 782 " --> pdb=" O VAL A1166 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A1154 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A1167 " --> pdb=" O THR A1191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A1191 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 4.196A 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 1172 through 1174 Processing sheet with id=AB6, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.756A pdb=" N ALA B 45 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 175 removed outlier: 4.450A pdb=" N GLY B 79 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 207 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 270 through 286 removed outlier: 7.279A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 283 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 440 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.640A 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: 7.279A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 283 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 7.048A 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: 6.875A pdb=" N HIS B 338 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 422 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 336 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 344 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 348 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 371 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 391 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 373 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 389 " --> pdb=" O CYS B 373 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 375 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE B 387 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 377 " --> pdb=" O TYR B 385 " (cutoff:3.500A) removed outlier: 5.958A 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: 4.216A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 738 " --> pdb=" O SER B 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.501A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 686 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 685 " --> pdb=" O TYR B 676 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 536 removed outlier: 4.016A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 550 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 549 " --> pdb=" O THR B 629 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 587 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE B 585 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 536 removed outlier: 4.016A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 550 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 549 " --> pdb=" O THR B 629 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 603 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER B 617 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 601 " --> pdb=" O SER B 617 " (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 786 removed outlier: 4.105A pdb=" N GLY B 780 " --> pdb=" O ALA B1168 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B1167 " --> pdb=" O THR B1191 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B1189 " --> pdb=" O ILE B1169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 789 through 798 removed outlier: 3.534A pdb=" N SER B 791 " --> pdb=" O VAL B1157 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B1155 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (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: 3.599A pdb=" N ILE B1178 " --> pdb=" O VAL B1174 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AD3, first strand: chain 'C' and resid 45 through 48 removed outlier: 3.549A pdb=" N ALA C 45 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.957A pdb=" N GLY C 69 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS C 196 " --> pdb=" O GLY C 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AD6, first strand: chain 'C' and resid 180 through 184 removed outlier: 3.538A pdb=" N VAL C 175 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 165 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.616A pdb=" N LEU C 109 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.639A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 440 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 401 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 408 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 270 through 288 removed outlier: 5.639A pdb=" N LYS C 272 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 453 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL C 274 " --> pdb=" O ILE C 451 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE C 451 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN C 276 " --> pdb=" O ALA C 449 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA C 449 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 447 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N SER C 443 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU C 284 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 441 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 286 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP C 439 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP C 448 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR C 463 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 450 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 461 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU C 452 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.667A pdb=" N GLN C 295 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 293 through 298 removed outlier: 3.667A pdb=" N GLN C 295 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS C 338 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL C 422 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 336 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 382 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.520A pdb=" N PHE C 734 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.556A pdb=" N THR C 550 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 519 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 549 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS C 587 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY C 625 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE C 585 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.556A pdb=" N THR C 550 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 519 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE C 549 " --> pdb=" O THR C 629 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR C 616 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 567 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 606 " --> pdb=" O SER C 565 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 650 through 654 removed outlier: 4.266A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 747 through 751 Processing sheet with id=AE8, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.886A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C1155 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.886A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C1155 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C1189 " --> pdb=" O ILE C1169 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF2, first strand: chain 'C' and resid 1220 through 1223 removed outlier: 3.580A pdb=" N THR C1181 " --> pdb=" O VAL C1221 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA C1179 " --> pdb=" O ILE C1223 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N CYS C1173 " --> pdb=" O LEU C1233 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2583 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 2.81 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: 7636 1.34 - 1.47: 6444 1.47 - 1.59: 10688 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 24918 Sorted by residual: bond pdb=" C LYS B 633 " pdb=" N PRO B 634 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.89e+00 bond pdb=" C ALA C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" C TYR A 751 " pdb=" N SER A 752 " ideal model delta sigma weight residual 1.325 1.337 -0.012 1.14e-02 7.69e+03 1.12e+00 bond pdb=" CA ASP C 466 " pdb=" CB ASP C 466 " ideal model delta sigma weight residual 1.525 1.540 -0.015 1.52e-02 4.33e+03 9.64e-01 bond pdb=" CA VAL A 750 " pdb=" CB VAL A 750 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 9.56e-01 ... (remaining 24913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 33577 2.33 - 4.67: 280 4.67 - 7.00: 23 7.00 - 9.34: 4 9.34 - 11.67: 1 Bond angle restraints: 33885 Sorted by residual: angle pdb=" N VAL C 748 " pdb=" CA VAL C 748 " pdb=" C VAL C 748 " ideal model delta sigma weight residual 111.62 108.07 3.55 7.90e-01 1.60e+00 2.01e+01 angle pdb=" N VAL A 748 " pdb=" CA VAL A 748 " pdb=" C VAL A 748 " ideal model delta sigma weight residual 111.56 108.13 3.43 8.60e-01 1.35e+00 1.59e+01 angle pdb=" C2 NAG C1410 " pdb=" N2 NAG C1410 " pdb=" C7 NAG C1410 " ideal model delta sigma weight residual 124.56 136.23 -11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C ALA B 232 " pdb=" N ASN B 233 " pdb=" CA ASN B 233 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ALA A 232 " pdb=" N ASN A 233 " pdb=" CA ASN A 233 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.45e+01 ... (remaining 33880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 14821 24.75 - 49.49: 480 49.49 - 74.24: 89 74.24 - 98.98: 14 98.98 - 123.73: 3 Dihedral angle restraints: 15407 sinusoidal: 6472 harmonic: 8935 Sorted by residual: dihedral pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " pdb=" SG CYS C 234 " pdb=" CB CYS C 234 " ideal model delta sinusoidal sigma weight residual 93.00 175.41 -82.41 1 1.00e+01 1.00e-02 8.33e+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 93.00 166.07 -73.07 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 700 " pdb=" CB CYS C 700 " ideal model delta sinusoidal sigma weight residual -86.00 -14.89 -71.11 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 15404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3447 0.060 - 0.120: 599 0.120 - 0.180: 64 0.180 - 0.239: 6 0.239 - 0.299: 1 Chirality restraints: 4117 Sorted by residual: chirality pdb=" C2 NAG C1410 " pdb=" C1 NAG C1410 " pdb=" C3 NAG C1410 " pdb=" N2 NAG C1410 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.24e+00 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 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 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 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4114 not shown) Planarity restraints: 4286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 277 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 278 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 278 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 278 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 277 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 278 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 278 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 278 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 466 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 467 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 467 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 467 " 0.025 5.00e-02 4.00e+02 ... (remaining 4283 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 9052 2.90 - 3.40: 21613 3.40 - 3.90: 38808 3.90 - 4.40: 42677 4.40 - 4.90: 74799 Nonbonded interactions: 186949 Sorted by model distance: nonbonded pdb=" O5 MAN K 4 " pdb=" O6 MAN K 4 " model vdw 2.395 2.432 nonbonded pdb=" O5 MAN F 5 " pdb=" O6 MAN F 5 " model vdw 2.531 2.432 nonbonded pdb=" O5 MAN J 5 " pdb=" O6 MAN J 5 " model vdw 2.559 2.432 nonbonded pdb=" C3 MAN K 5 " pdb=" O5 MAN K 5 " model vdw 2.574 2.776 nonbonded pdb=" O ARG C1183 " pdb=" CA GLU C1184 " model vdw 2.603 2.776 ... (remaining 186944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 520 or resid 528 through 1407)) selection = (chain 'B' and (resid 33 through 330 or resid 334 through 1407)) selection = (chain 'C' and (resid 33 through 54 or resid 67 through 73 or resid 77 through 8 \ 2 or resid 163 through 168 or resid 173 through 178 or resid 205 through 219 or \ resid 225 through 290 or resid 294 through 330 or resid 334 through 355 or resid \ 369 through 426 or resid 437 through 880 or resid 894 through 904 or resid 915 \ through 966 or resid 971 through 989 or resid 996 through 1014 or resid 1026 thr \ ough 1231 or resid 1405 through 1411)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.600 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.002 0.048 25014 Z= 0.118 Angle : 0.569 11.674 34131 Z= 0.291 Chirality : 0.045 0.299 4117 Planarity : 0.004 0.048 4250 Dihedral : 12.126 123.726 9533 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.75 (0.15), residues: 2990 helix: 0.75 (0.20), residues: 611 sheet: -0.19 (0.21), residues: 732 loop : -1.12 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1183 TYR 0.026 0.001 TYR A 606 PHE 0.012 0.001 PHE B1141 TRP 0.012 0.001 TRP C 259 HIS 0.003 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (24918) covalent geometry : angle 0.55628 / 0.29 (33885) SS BOND : bond 0.00237 / 0.16 ( 42) SS BOND : angle 1.41548 / 0.95 ( 84) hydrogen bonds : bond 0.20915 / 13.63 ( 850) hydrogen bonds : angle 8.43894 / 5.85 ( 2583) link_ALPHA1-3 : bond 0.00847 / 0.43 ( 3) link_ALPHA1-3 : angle 1.55414 / 1.10 ( 9) link_ALPHA1-6 : bond 0.00830 / 0.42 ( 3) link_ALPHA1-6 : angle 1.25240 / 0.96 ( 9) link_BETA1-4 : bond 0.00314 / 0.21 ( 12) link_BETA1-4 : angle 1.61358 / 1.15 ( 36) link_NAG-ASN : bond 0.00215 / 0.14 ( 36) link_NAG-ASN : angle 1.61629 / 1.07 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 833 time to evaluate : 0.835 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 272 LYS cc_start: 0.7918 (mttt) cc_final: 0.7585 (mttm) REVERT: A 396 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7648 (mtt180) REVERT: A 420 ASP cc_start: 0.7281 (p0) cc_final: 0.7029 (t0) REVERT: A 444 THR cc_start: 0.8020 (p) cc_final: 0.7395 (p) REVERT: A 445 ASN cc_start: 0.8298 (m-40) cc_final: 0.7876 (m-40) REVERT: A 463 TYR cc_start: 0.7616 (m-10) cc_final: 0.7263 (m-80) REVERT: A 546 THR cc_start: 0.7734 (p) cc_final: 0.7463 (p) REVERT: A 556 ASN cc_start: 0.5005 (t0) cc_final: 0.4616 (t0) REVERT: A 578 SER cc_start: 0.8487 (m) cc_final: 0.8036 (t) REVERT: A 615 PHE cc_start: 0.7761 (m-80) cc_final: 0.7072 (m-80) REVERT: A 651 LYS cc_start: 0.8367 (tttt) cc_final: 0.8151 (tttt) REVERT: A 669 SER cc_start: 0.8505 (t) cc_final: 0.8009 (p) REVERT: A 674 VAL cc_start: 0.8743 (m) cc_final: 0.8325 (t) REVERT: A 704 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6159 (mt-10) REVERT: A 723 SER cc_start: 0.8097 (t) cc_final: 0.7748 (m) REVERT: A 739 ASN cc_start: 0.8137 (m-40) cc_final: 0.7662 (m-40) REVERT: A 795 GLU cc_start: 0.7138 (tt0) cc_final: 0.6900 (tt0) REVERT: A 802 THR cc_start: 0.8511 (m) cc_final: 0.8284 (p) REVERT: A 814 ASN cc_start: 0.8406 (t0) cc_final: 0.8202 (t0) REVERT: A 844 GLU cc_start: 0.7404 (tp30) cc_final: 0.7091 (tp30) REVERT: A 857 GLU cc_start: 0.7645 (mp0) cc_final: 0.6645 (mp0) REVERT: A 860 GLN cc_start: 0.7455 (pt0) cc_final: 0.7228 (tm-30) REVERT: A 861 LEU cc_start: 0.8512 (mt) cc_final: 0.8274 (tp) REVERT: A 870 ASP cc_start: 0.6210 (t70) cc_final: 0.5914 (t0) REVERT: A 924 ARG cc_start: 0.7232 (mmp-170) cc_final: 0.6970 (mmp-170) REVERT: A 954 SER cc_start: 0.8640 (m) cc_final: 0.8290 (p) REVERT: A 962 VAL cc_start: 0.7724 (m) cc_final: 0.7312 (t) REVERT: A 999 LEU cc_start: 0.8290 (mt) cc_final: 0.8045 (tp) REVERT: A 1007 ILE cc_start: 0.8492 (tp) cc_final: 0.8245 (tp) REVERT: A 1011 THR cc_start: 0.8499 (m) cc_final: 0.8252 (m) REVERT: A 1040 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 1050 SER cc_start: 0.7780 (m) cc_final: 0.7519 (p) REVERT: A 1071 TYR cc_start: 0.7922 (m-80) cc_final: 0.7549 (m-80) REVERT: A 1074 LEU cc_start: 0.8714 (mt) cc_final: 0.8351 (mp) REVERT: A 1084 ASP cc_start: 0.6752 (t70) cc_final: 0.6331 (t0) REVERT: A 1085 ARG cc_start: 0.7435 (ptp-110) cc_final: 0.7200 (ptp90) REVERT: A 1118 LYS cc_start: 0.7813 (mmtp) cc_final: 0.7423 (mmtp) REVERT: A 1144 VAL cc_start: 0.8738 (t) cc_final: 0.8532 (m) REVERT: A 1169 ILE cc_start: 0.8246 (mt) cc_final: 0.7821 (mm) REVERT: A 1203 PHE cc_start: 0.8273 (m-80) cc_final: 0.7937 (m-80) REVERT: A 1223 ILE cc_start: 0.7434 (pt) cc_final: 0.7113 (mt) REVERT: B 81 PHE cc_start: 0.7101 (m-80) cc_final: 0.6769 (m-10) REVERT: B 214 MET cc_start: 0.7007 (tpt) cc_final: 0.6660 (tpt) REVERT: B 233 ASN cc_start: 0.8218 (p0) cc_final: 0.7935 (p0) REVERT: B 247 ASN cc_start: 0.7980 (p0) cc_final: 0.7583 (p0) REVERT: B 257 ASN cc_start: 0.7496 (t0) cc_final: 0.7124 (t0) REVERT: B 285 LEU cc_start: 0.8745 (pp) cc_final: 0.8483 (pt) REVERT: B 348 VAL cc_start: 0.8420 (m) cc_final: 0.8185 (p) REVERT: B 351 ASN cc_start: 0.7151 (p0) cc_final: 0.6756 (p0) REVERT: B 376 LYS cc_start: 0.8059 (tttm) cc_final: 0.7831 (mtpp) REVERT: B 386 LYS cc_start: 0.7265 (mtpt) cc_final: 0.7040 (mtpt) REVERT: B 402 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8053 (ptmm) REVERT: B 459 GLN cc_start: 0.7868 (mm110) cc_final: 0.7533 (mm-40) REVERT: B 462 LEU cc_start: 0.8004 (tp) cc_final: 0.7790 (tp) REVERT: B 463 TYR cc_start: 0.7960 (m-10) cc_final: 0.7723 (m-80) REVERT: B 465 ASP cc_start: 0.7061 (m-30) cc_final: 0.6844 (m-30) REVERT: B 509 ASP cc_start: 0.7403 (t0) cc_final: 0.7110 (p0) REVERT: B 515 ILE cc_start: 0.8421 (mt) cc_final: 0.8189 (pt) REVERT: B 535 THR cc_start: 0.7710 (p) cc_final: 0.7399 (t) REVERT: B 578 SER cc_start: 0.7811 (m) cc_final: 0.7349 (t) REVERT: B 587 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7743 (ttpp) REVERT: B 660 GLU cc_start: 0.6740 (mp0) cc_final: 0.6458 (mp0) REVERT: B 668 SER cc_start: 0.8887 (t) cc_final: 0.8495 (p) REVERT: B 670 PHE cc_start: 0.8077 (m-10) cc_final: 0.7752 (m-80) REVERT: B 749 LEU cc_start: 0.8043 (mt) cc_final: 0.7749 (mt) REVERT: B 802 THR cc_start: 0.8774 (m) cc_final: 0.8286 (p) REVERT: B 847 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6929 (mt-10) REVERT: B 848 VAL cc_start: 0.7814 (t) cc_final: 0.7568 (t) REVERT: B 855 SER cc_start: 0.8085 (t) cc_final: 0.7869 (m) REVERT: B 939 MET cc_start: 0.8377 (mtm) cc_final: 0.8132 (mtm) REVERT: B 983 ASN cc_start: 0.7105 (t0) cc_final: 0.6816 (t0) REVERT: B 1061 GLN cc_start: 0.6910 (mp-120) cc_final: 0.6601 (mp-120) REVERT: B 1069 ASP cc_start: 0.7184 (t0) cc_final: 0.6975 (t0) REVERT: B 1084 ASP cc_start: 0.7101 (t70) cc_final: 0.6481 (t0) REVERT: B 1085 ARG cc_start: 0.7483 (ptp-110) cc_final: 0.7007 (ptp90) REVERT: B 1107 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7043 (mt-10) REVERT: B 1117 GLN cc_start: 0.7617 (mt0) cc_final: 0.7359 (tt0) REVERT: C 35 PHE cc_start: 0.8556 (t80) cc_final: 0.8344 (t80) REVERT: C 161 HIS cc_start: 0.7131 (m-70) cc_final: 0.6789 (m170) REVERT: C 179 LYS cc_start: 0.7851 (pttp) cc_final: 0.7602 (pttm) REVERT: C 185 PHE cc_start: 0.7838 (t80) cc_final: 0.7550 (t80) REVERT: C 204 MET cc_start: 0.5832 (mtt) cc_final: 0.5592 (mtt) REVERT: C 211 THR cc_start: 0.7739 (m) cc_final: 0.7301 (p) REVERT: C 226 SER cc_start: 0.8589 (m) cc_final: 0.8356 (t) REVERT: C 247 ASN cc_start: 0.8042 (p0) cc_final: 0.7510 (p0) REVERT: C 285 LEU cc_start: 0.8523 (mt) cc_final: 0.8209 (mp) REVERT: C 287 ILE cc_start: 0.8448 (mp) cc_final: 0.8200 (mm) REVERT: C 343 THR cc_start: 0.8049 (m) cc_final: 0.7810 (p) REVERT: C 354 ASP cc_start: 0.7185 (t0) cc_final: 0.6803 (t0) REVERT: C 377 VAL cc_start: 0.8544 (t) cc_final: 0.8153 (t) REVERT: C 463 TYR cc_start: 0.8204 (m-80) cc_final: 0.7848 (m-80) REVERT: C 466 ASP cc_start: 0.7345 (p0) cc_final: 0.7009 (p0) REVERT: C 478 PHE cc_start: 0.8558 (m-80) cc_final: 0.8299 (m-80) REVERT: C 487 ILE cc_start: 0.7862 (pt) cc_final: 0.7611 (mt) REVERT: C 499 ILE cc_start: 0.8221 (mm) cc_final: 0.7993 (tt) REVERT: C 512 PHE cc_start: 0.7018 (m-80) cc_final: 0.6682 (m-80) REVERT: C 546 THR cc_start: 0.7926 (p) cc_final: 0.7702 (t) REVERT: C 569 ASP cc_start: 0.7770 (t70) cc_final: 0.7534 (t0) REVERT: C 581 ASP cc_start: 0.7175 (t0) cc_final: 0.6829 (t0) REVERT: C 590 VAL cc_start: 0.8692 (t) cc_final: 0.8343 (m) REVERT: C 603 LEU cc_start: 0.8247 (mt) cc_final: 0.7882 (mm) REVERT: C 615 PHE cc_start: 0.7999 (m-80) cc_final: 0.7554 (m-80) REVERT: C 626 GLU cc_start: 0.6050 (mp0) cc_final: 0.5651 (mp0) REVERT: C 640 ASP cc_start: 0.6843 (t0) cc_final: 0.6587 (t70) REVERT: C 651 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8139 (ttmm) REVERT: C 704 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6762 (mt-10) REVERT: C 709 VAL cc_start: 0.8257 (t) cc_final: 0.7073 (t) REVERT: C 772 VAL cc_start: 0.7985 (p) cc_final: 0.7604 (m) REVERT: C 790 MET cc_start: 0.8051 (mtt) cc_final: 0.7607 (mtp) REVERT: C 820 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7463 (mttp) REVERT: C 843 LEU cc_start: 0.8168 (tp) cc_final: 0.7866 (tt) REVERT: C 874 PHE cc_start: 0.8067 (m-80) cc_final: 0.7625 (m-80) REVERT: C 876 ASN cc_start: 0.8151 (m-40) cc_final: 0.7922 (m-40) REVERT: C 899 ASP cc_start: 0.7416 (m-30) cc_final: 0.7091 (m-30) REVERT: C 928 ASP cc_start: 0.7561 (p0) cc_final: 0.7265 (p0) REVERT: C 957 LEU cc_start: 0.8247 (mt) cc_final: 0.7983 (mp) REVERT: C 976 TYR cc_start: 0.7967 (m-10) cc_final: 0.7710 (m-10) REVERT: C 1061 GLN cc_start: 0.7437 (mp10) cc_final: 0.7189 (mp10) REVERT: C 1069 ASP cc_start: 0.6344 (t0) cc_final: 0.5958 (t0) REVERT: C 1127 SER cc_start: 0.7862 (t) cc_final: 0.7163 (p) REVERT: C 1128 GLN cc_start: 0.7332 (mp-120) cc_final: 0.7061 (mp-120) REVERT: C 1181 THR cc_start: 0.8408 (t) cc_final: 0.8146 (m) REVERT: C 1213 ARG cc_start: 0.8113 (ptt180) cc_final: 0.7810 (ptt-90) REVERT: C 1220 PHE cc_start: 0.7986 (m-80) cc_final: 0.7488 (m-80) REVERT: C 1221 VAL cc_start: 0.8167 (m) cc_final: 0.7864 (p) outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 0.1555 time to fit residues: 204.7533 Evaluate side-chains 594 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 GLN A 682 GLN A1100 GLN A1109 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 338 HIS B 568 GLN B 577 GLN B 621 GLN B 771 GLN B 814 ASN C 40 ASN C 42 GLN C 71 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 GLN C 996 GLN C1120 ASN ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095023 restraints weight = 41532.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098130 restraints weight = 20676.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100189 restraints weight = 12353.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101356 restraints weight = 8427.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102357 restraints weight = 6531.577| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25014 Z= 0.287 Angle : 0.698 12.674 34131 Z= 0.360 Chirality : 0.048 0.268 4117 Planarity : 0.005 0.053 4250 Dihedral : 7.020 113.269 4385 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.24 % Allowed : 10.36 % Favored : 87.39 % 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: 2990 helix: 1.11 (0.20), residues: 627 sheet: -0.30 (0.20), residues: 714 loop : -1.18 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1235 TYR 0.031 0.002 TYR A 606 PHE 0.028 0.002 PHE B1190 TRP 0.020 0.002 TRP C 259 HIS 0.010 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.29 (24918) covalent geometry : angle 0.67438 / 0.35 (33885) SS BOND : bond 0.00595 / 0.36 ( 42) SS BOND : angle 2.72357 / 1.68 ( 84) hydrogen bonds : bond 0.05100 / 3.39 ( 850) hydrogen bonds : angle 5.91222 / 4.03 ( 2583) link_ALPHA1-3 : bond 0.00553 / 0.28 ( 3) link_ALPHA1-3 : angle 1.82013 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00681 / 0.34 ( 3) link_ALPHA1-6 : angle 1.60209 / 1.03 ( 9) link_BETA1-4 : bond 0.00410 / 0.25 ( 12) link_BETA1-4 : angle 2.03101 / 1.43 ( 36) link_NAG-ASN : bond 0.00492 / 0.30 ( 36) link_NAG-ASN : angle 1.93000 / 1.26 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 623 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6337 (m-80) cc_final: 0.6117 (t80) REVERT: A 176 PHE cc_start: 0.7626 (m-80) cc_final: 0.7326 (m-80) REVERT: A 213 TYR cc_start: 0.6849 (m-80) cc_final: 0.6637 (m-80) REVERT: A 276 ASN cc_start: 0.7565 (t0) cc_final: 0.7002 (p0) REVERT: A 396 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7828 (mtt180) REVERT: A 444 THR cc_start: 0.7917 (p) cc_final: 0.7641 (p) REVERT: A 445 ASN cc_start: 0.8367 (m-40) cc_final: 0.8096 (m-40) REVERT: A 470 GLN cc_start: 0.8307 (tt0) cc_final: 0.7986 (tt0) REVERT: A 482 ASP cc_start: 0.6915 (m-30) cc_final: 0.6634 (p0) REVERT: A 509 ASP cc_start: 0.7064 (p0) cc_final: 0.6591 (p0) REVERT: A 578 SER cc_start: 0.8522 (m) cc_final: 0.8111 (p) REVERT: A 615 PHE cc_start: 0.7834 (m-80) cc_final: 0.7590 (m-80) REVERT: A 638 VAL cc_start: 0.8737 (t) cc_final: 0.8448 (p) REVERT: A 644 MET cc_start: 0.7462 (ptp) cc_final: 0.7252 (ptt) REVERT: A 651 LYS cc_start: 0.8362 (tttt) cc_final: 0.7874 (ttpt) REVERT: A 669 SER cc_start: 0.8330 (t) cc_final: 0.7920 (p) REVERT: A 674 VAL cc_start: 0.8912 (m) cc_final: 0.8575 (t) REVERT: A 687 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8309 (tttp) REVERT: A 704 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6186 (mt-10) REVERT: A 723 SER cc_start: 0.8159 (t) cc_final: 0.7940 (p) REVERT: A 739 ASN cc_start: 0.8043 (m-40) cc_final: 0.7818 (m110) REVERT: A 856 GLU cc_start: 0.7090 (pm20) cc_final: 0.6429 (pm20) REVERT: A 857 GLU cc_start: 0.7684 (mp0) cc_final: 0.6804 (mp0) REVERT: A 870 ASP cc_start: 0.6180 (t70) cc_final: 0.5971 (t0) REVERT: A 898 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6773 (mm-30) REVERT: A 924 ARG cc_start: 0.7280 (mmp-170) cc_final: 0.7017 (mmt180) REVERT: A 951 HIS cc_start: 0.8014 (t70) cc_final: 0.7516 (t-90) REVERT: A 954 SER cc_start: 0.8675 (m) cc_final: 0.8344 (p) REVERT: A 962 VAL cc_start: 0.8002 (m) cc_final: 0.7667 (t) REVERT: A 998 LEU cc_start: 0.8646 (tt) cc_final: 0.8008 (tp) REVERT: A 1050 SER cc_start: 0.7888 (m) cc_final: 0.7617 (p) REVERT: A 1104 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7866 (mmtp) REVERT: A 1113 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7834 (mtpp) REVERT: A 1118 LYS cc_start: 0.7949 (mmtp) cc_final: 0.7663 (mttp) REVERT: A 1144 VAL cc_start: 0.8714 (t) cc_final: 0.8510 (m) REVERT: A 1211 GLU cc_start: 0.7163 (mp0) cc_final: 0.6938 (mp0) REVERT: A 1223 ILE cc_start: 0.7220 (pt) cc_final: 0.6975 (mt) REVERT: A 1230 TYR cc_start: 0.7511 (m-80) cc_final: 0.7239 (m-80) REVERT: B 81 PHE cc_start: 0.7046 (m-80) cc_final: 0.6784 (m-10) REVERT: B 214 MET cc_start: 0.7038 (tpt) cc_final: 0.6824 (tpt) REVERT: B 247 ASN cc_start: 0.8065 (p0) cc_final: 0.7718 (p0) REVERT: B 257 ASN cc_start: 0.7829 (t0) cc_final: 0.7416 (t0) REVERT: B 272 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: B 351 ASN cc_start: 0.7169 (p0) cc_final: 0.6940 (p0) REVERT: B 420 ASP cc_start: 0.7312 (t0) cc_final: 0.7079 (t0) REVERT: B 459 GLN cc_start: 0.8002 (mm110) cc_final: 0.7783 (mm-40) REVERT: B 509 ASP cc_start: 0.7572 (t0) cc_final: 0.6982 (p0) REVERT: B 510 HIS cc_start: 0.8103 (t-90) cc_final: 0.7704 (t-170) REVERT: B 651 LYS cc_start: 0.8077 (tttt) cc_final: 0.7603 (mmmm) REVERT: B 660 GLU cc_start: 0.6699 (mp0) cc_final: 0.6180 (mp0) REVERT: B 668 SER cc_start: 0.8883 (t) cc_final: 0.8517 (p) REVERT: B 670 PHE cc_start: 0.8318 (m-10) cc_final: 0.7687 (m-80) REVERT: B 710 ASP cc_start: 0.7012 (m-30) cc_final: 0.6494 (m-30) REVERT: B 740 ASP cc_start: 0.6966 (t0) cc_final: 0.6639 (t0) REVERT: B 757 CYS cc_start: 0.6119 (t) cc_final: 0.5745 (t) REVERT: B 758 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8299 (ttmm) REVERT: B 768 GLN cc_start: 0.7509 (mt0) cc_final: 0.7220 (mt0) REVERT: B 844 GLU cc_start: 0.7566 (tp30) cc_final: 0.7198 (tp30) REVERT: B 847 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7110 (mt-10) REVERT: B 855 SER cc_start: 0.7915 (t) cc_final: 0.7661 (m) REVERT: B 954 SER cc_start: 0.8429 (m) cc_final: 0.7996 (p) REVERT: B 983 ASN cc_start: 0.7155 (t0) cc_final: 0.6917 (t0) REVERT: B 1061 GLN cc_start: 0.7058 (mp-120) cc_final: 0.6837 (mp-120) REVERT: B 1069 ASP cc_start: 0.7114 (t0) cc_final: 0.6800 (t0) REVERT: B 1073 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: B 1074 LEU cc_start: 0.8614 (mt) cc_final: 0.8344 (mp) REVERT: B 1084 ASP cc_start: 0.7185 (t70) cc_final: 0.6878 (t0) REVERT: B 1107 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7160 (mt-10) REVERT: C 35 PHE cc_start: 0.8401 (t80) cc_final: 0.8167 (t80) REVERT: C 42 GLN cc_start: 0.6785 (tp-100) cc_final: 0.6398 (tp40) REVERT: C 179 LYS cc_start: 0.7554 (pttp) cc_final: 0.7168 (pttm) REVERT: C 181 TYR cc_start: 0.7677 (m-80) cc_final: 0.6889 (m-80) REVERT: C 185 PHE cc_start: 0.8056 (t80) cc_final: 0.7705 (t80) REVERT: C 204 MET cc_start: 0.6182 (mtt) cc_final: 0.5915 (mtt) REVERT: C 209 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7180 (mm-30) REVERT: C 211 THR cc_start: 0.7859 (m) cc_final: 0.7527 (p) REVERT: C 213 TYR cc_start: 0.7790 (m-80) cc_final: 0.7192 (m-80) REVERT: C 247 ASN cc_start: 0.7984 (p0) cc_final: 0.7630 (p0) REVERT: C 284 LEU cc_start: 0.8471 (tp) cc_final: 0.8260 (tt) REVERT: C 287 ILE cc_start: 0.8480 (mp) cc_final: 0.8226 (mm) REVERT: C 291 TYR cc_start: 0.7681 (m-10) cc_final: 0.7090 (m-10) REVERT: C 354 ASP cc_start: 0.6971 (t0) cc_final: 0.6342 (t0) REVERT: C 463 TYR cc_start: 0.8275 (m-80) cc_final: 0.7960 (m-80) REVERT: C 499 ILE cc_start: 0.8430 (mm) cc_final: 0.8070 (tt) REVERT: C 512 PHE cc_start: 0.6953 (m-80) cc_final: 0.6534 (m-80) REVERT: C 555 TYR cc_start: 0.6796 (m-80) cc_final: 0.6155 (m-80) REVERT: C 569 ASP cc_start: 0.7568 (t70) cc_final: 0.7206 (t0) REVERT: C 581 ASP cc_start: 0.7352 (t0) cc_final: 0.6793 (t0) REVERT: C 590 VAL cc_start: 0.8715 (t) cc_final: 0.8379 (m) REVERT: C 591 SER cc_start: 0.7884 (t) cc_final: 0.7592 (t) REVERT: C 603 LEU cc_start: 0.8407 (mt) cc_final: 0.8068 (mm) REVERT: C 615 PHE cc_start: 0.8095 (m-80) cc_final: 0.7362 (m-80) REVERT: C 616 THR cc_start: 0.8417 (t) cc_final: 0.8119 (m) REVERT: C 626 GLU cc_start: 0.6309 (mp0) cc_final: 0.5916 (mp0) REVERT: C 651 LYS cc_start: 0.8546 (ttpt) cc_final: 0.7991 (ttmm) REVERT: C 660 GLU cc_start: 0.7490 (mp0) cc_final: 0.7146 (mp0) REVERT: C 704 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 772 VAL cc_start: 0.7948 (p) cc_final: 0.7735 (m) REVERT: C 843 LEU cc_start: 0.8184 (tp) cc_final: 0.7973 (tt) REVERT: C 856 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6878 (tp30) REVERT: C 874 PHE cc_start: 0.8093 (m-80) cc_final: 0.7676 (m-80) REVERT: C 876 ASN cc_start: 0.8199 (m-40) cc_final: 0.7957 (m-40) REVERT: C 899 ASP cc_start: 0.7443 (m-30) cc_final: 0.6962 (m-30) REVERT: C 957 LEU cc_start: 0.8324 (mt) cc_final: 0.8091 (mp) REVERT: C 979 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7551 (tp40) REVERT: C 1001 GLU cc_start: 0.7519 (tp30) cc_final: 0.6970 (tp30) REVERT: C 1043 ASN cc_start: 0.7382 (p0) cc_final: 0.7096 (p0) REVERT: C 1127 SER cc_start: 0.7961 (t) cc_final: 0.7659 (p) REVERT: C 1156 THR cc_start: 0.8270 (m) cc_final: 0.7846 (p) REVERT: C 1181 THR cc_start: 0.8462 (t) cc_final: 0.8140 (m) REVERT: C 1220 PHE cc_start: 0.7915 (m-80) cc_final: 0.7556 (m-80) REVERT: C 1236 ASP cc_start: 0.7862 (p0) cc_final: 0.7267 (p0) outliers start: 60 outliers final: 36 residues processed: 655 average time/residue: 0.1568 time to fit residues: 161.3376 Evaluate side-chains 603 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 566 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1184 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 275 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN A1139 HIS B 814 ASN B1095 ASN B1139 HIS C 40 ASN C 814 ASN C 996 GLN C1120 ASN ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101797 restraints weight = 39978.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105205 restraints weight = 19269.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107421 restraints weight = 11224.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108866 restraints weight = 7523.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109653 restraints weight = 5623.349| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25014 Z= 0.155 Angle : 0.596 9.627 34131 Z= 0.304 Chirality : 0.044 0.257 4117 Planarity : 0.004 0.041 4250 Dihedral : 6.669 110.012 4385 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.77 % Allowed : 12.27 % Favored : 84.96 % 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: -0.56 (0.15), residues: 2990 helix: 1.41 (0.20), residues: 627 sheet: -0.38 (0.20), residues: 763 loop : -1.09 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1207 TYR 0.022 0.001 TYR A 606 PHE 0.029 0.001 PHE A 507 TRP 0.014 0.001 TRP C 168 HIS 0.011 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (24918) covalent geometry : angle 0.57679 / 0.30 (33885) SS BOND : bond 0.00507 / 0.33 ( 42) SS BOND : angle 2.25049 / 1.42 ( 84) hydrogen bonds : bond 0.04346 / 2.88 ( 850) hydrogen bonds : angle 5.47529 / 3.72 ( 2583) link_ALPHA1-3 : bond 0.00812 / 0.41 ( 3) link_ALPHA1-3 : angle 1.80461 / 1.30 ( 9) link_ALPHA1-6 : bond 0.00849 / 0.42 ( 3) link_ALPHA1-6 : angle 1.52160 / 1.04 ( 9) link_BETA1-4 : bond 0.00278 / 0.15 ( 12) link_BETA1-4 : angle 1.59220 / 1.15 ( 36) link_NAG-ASN : bond 0.00245 / 0.16 ( 36) link_NAG-ASN : angle 1.67805 / 1.13 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 602 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6302 (m-80) cc_final: 0.6011 (t80) REVERT: A 176 PHE cc_start: 0.7743 (m-80) cc_final: 0.7328 (m-80) REVERT: A 212 TYR cc_start: 0.8159 (m-80) cc_final: 0.7924 (m-10) REVERT: A 213 TYR cc_start: 0.6863 (m-80) cc_final: 0.6384 (m-80) REVERT: A 276 ASN cc_start: 0.7308 (t0) cc_final: 0.6730 (p0) REVERT: A 396 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7637 (mtt180) REVERT: A 444 THR cc_start: 0.7747 (p) cc_final: 0.7502 (p) REVERT: A 445 ASN cc_start: 0.8372 (m-40) cc_final: 0.8053 (m-40) REVERT: A 470 GLN cc_start: 0.8213 (tt0) cc_final: 0.7917 (tt0) REVERT: A 482 ASP cc_start: 0.6795 (m-30) cc_final: 0.6541 (p0) REVERT: A 509 ASP cc_start: 0.7184 (p0) cc_final: 0.6719 (p0) REVERT: A 556 ASN cc_start: 0.5136 (t0) cc_final: 0.4739 (t0) REVERT: A 578 SER cc_start: 0.8482 (m) cc_final: 0.8025 (p) REVERT: A 615 PHE cc_start: 0.7812 (m-80) cc_final: 0.7596 (m-80) REVERT: A 638 VAL cc_start: 0.8739 (t) cc_final: 0.8431 (p) REVERT: A 644 MET cc_start: 0.7509 (ptp) cc_final: 0.7208 (ptt) REVERT: A 651 LYS cc_start: 0.8385 (tttt) cc_final: 0.7806 (ttpt) REVERT: A 669 SER cc_start: 0.8292 (t) cc_final: 0.7815 (p) REVERT: A 674 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8487 (t) REVERT: A 687 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8285 (tttp) REVERT: A 739 ASN cc_start: 0.8033 (m-40) cc_final: 0.7813 (m110) REVERT: A 746 GLU cc_start: 0.7665 (mp0) cc_final: 0.7391 (mp0) REVERT: A 851 MET cc_start: 0.7607 (ttm) cc_final: 0.7194 (ttp) REVERT: A 856 GLU cc_start: 0.7131 (pm20) cc_final: 0.6493 (pm20) REVERT: A 857 GLU cc_start: 0.7669 (mp0) cc_final: 0.6817 (mp0) REVERT: A 870 ASP cc_start: 0.6267 (t70) cc_final: 0.5973 (t0) REVERT: A 898 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6705 (mm-30) REVERT: A 924 ARG cc_start: 0.7313 (mmp-170) cc_final: 0.7001 (mmt180) REVERT: A 948 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6249 (tm-30) REVERT: A 951 HIS cc_start: 0.7961 (t70) cc_final: 0.7570 (t-90) REVERT: A 954 SER cc_start: 0.8638 (m) cc_final: 0.8320 (p) REVERT: A 962 VAL cc_start: 0.8180 (m) cc_final: 0.7839 (t) REVERT: A 1040 GLU cc_start: 0.7333 (tm-30) cc_final: 0.7097 (tm-30) REVERT: A 1045 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7000 (tm-30) REVERT: A 1071 TYR cc_start: 0.7840 (m-80) cc_final: 0.7308 (m-80) REVERT: A 1104 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7744 (mmtp) REVERT: A 1107 GLU cc_start: 0.7401 (tp30) cc_final: 0.7160 (tp30) REVERT: A 1109 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7395 (tp40) REVERT: A 1113 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7776 (mtpp) REVERT: A 1144 VAL cc_start: 0.8696 (t) cc_final: 0.8465 (m) REVERT: A 1211 GLU cc_start: 0.7254 (mp0) cc_final: 0.6994 (mm-30) REVERT: A 1223 ILE cc_start: 0.7179 (pt) cc_final: 0.6931 (mt) REVERT: A 1230 TYR cc_start: 0.7529 (m-80) cc_final: 0.7117 (m-80) REVERT: B 33 ARG cc_start: 0.4514 (tmt170) cc_final: 0.4132 (tpt-90) REVERT: B 214 MET cc_start: 0.7041 (tpt) cc_final: 0.6721 (tpt) REVERT: B 237 TYR cc_start: 0.8382 (t80) cc_final: 0.8139 (t80) REVERT: B 247 ASN cc_start: 0.7992 (p0) cc_final: 0.7628 (p0) REVERT: B 257 ASN cc_start: 0.7798 (t0) cc_final: 0.7365 (t0) REVERT: B 272 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8144 (mttm) REVERT: B 351 ASN cc_start: 0.7212 (p0) cc_final: 0.6950 (p0) REVERT: B 376 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8258 (mtpp) REVERT: B 420 ASP cc_start: 0.7501 (t0) cc_final: 0.7201 (t0) REVERT: B 507 PHE cc_start: 0.7913 (p90) cc_final: 0.7432 (p90) REVERT: B 509 ASP cc_start: 0.7736 (t0) cc_final: 0.6955 (p0) REVERT: B 569 ASP cc_start: 0.8173 (t0) cc_final: 0.7925 (t0) REVERT: B 648 VAL cc_start: 0.8127 (t) cc_final: 0.7797 (m) REVERT: B 651 LYS cc_start: 0.8150 (tttt) cc_final: 0.7570 (mmmm) REVERT: B 660 GLU cc_start: 0.6687 (mp0) cc_final: 0.6184 (mp0) REVERT: B 668 SER cc_start: 0.8898 (t) cc_final: 0.8519 (p) REVERT: B 670 PHE cc_start: 0.8288 (m-10) cc_final: 0.7698 (m-80) REVERT: B 671 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 679 ASP cc_start: 0.7550 (m-30) cc_final: 0.7230 (m-30) REVERT: B 740 ASP cc_start: 0.6960 (t0) cc_final: 0.6495 (t0) REVERT: B 757 CYS cc_start: 0.6125 (t) cc_final: 0.5756 (t) REVERT: B 758 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8315 (ttmm) REVERT: B 768 GLN cc_start: 0.7556 (mt0) cc_final: 0.7314 (mt0) REVERT: B 820 LYS cc_start: 0.7384 (mttp) cc_final: 0.7037 (tppt) REVERT: B 844 GLU cc_start: 0.7629 (tp30) cc_final: 0.7112 (tp30) REVERT: B 847 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 954 SER cc_start: 0.8315 (m) cc_final: 0.7887 (p) REVERT: B 983 ASN cc_start: 0.7255 (t0) cc_final: 0.7010 (t0) REVERT: B 1069 ASP cc_start: 0.7237 (t0) cc_final: 0.6607 (t0) REVERT: B 1084 ASP cc_start: 0.7228 (t70) cc_final: 0.6919 (t0) REVERT: B 1107 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7176 (mt-10) REVERT: B 1111 SER cc_start: 0.8096 (t) cc_final: 0.7869 (p) REVERT: B 1117 GLN cc_start: 0.7814 (mt0) cc_final: 0.7307 (tt0) REVERT: B 1184 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7151 (mm-30) REVERT: B 1190 PHE cc_start: 0.8387 (p90) cc_final: 0.7728 (p90) REVERT: B 1227 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7585 (t) REVERT: C 35 PHE cc_start: 0.8440 (t80) cc_final: 0.8165 (t80) REVERT: C 179 LYS cc_start: 0.7554 (pttp) cc_final: 0.7222 (pttm) REVERT: C 181 TYR cc_start: 0.7567 (m-80) cc_final: 0.7187 (m-10) REVERT: C 185 PHE cc_start: 0.7991 (t80) cc_final: 0.7623 (t80) REVERT: C 204 MET cc_start: 0.6340 (mtt) cc_final: 0.6037 (mtt) REVERT: C 211 THR cc_start: 0.7869 (m) cc_final: 0.7455 (p) REVERT: C 213 TYR cc_start: 0.7733 (m-80) cc_final: 0.7218 (m-80) REVERT: C 247 ASN cc_start: 0.7930 (p0) cc_final: 0.7377 (p0) REVERT: C 291 TYR cc_start: 0.7457 (m-10) cc_final: 0.7153 (m-10) REVERT: C 317 GLU cc_start: 0.7097 (tp30) cc_final: 0.6472 (tp30) REVERT: C 354 ASP cc_start: 0.6945 (t0) cc_final: 0.6273 (t0) REVERT: C 438 PHE cc_start: 0.8305 (m-80) cc_final: 0.7705 (m-80) REVERT: C 463 TYR cc_start: 0.8249 (m-80) cc_final: 0.7915 (m-80) REVERT: C 512 PHE cc_start: 0.6903 (m-80) cc_final: 0.6492 (m-80) REVERT: C 555 TYR cc_start: 0.6579 (m-80) cc_final: 0.6119 (m-80) REVERT: C 569 ASP cc_start: 0.7611 (t70) cc_final: 0.7124 (t0) REVERT: C 581 ASP cc_start: 0.7469 (t0) cc_final: 0.6863 (t0) REVERT: C 590 VAL cc_start: 0.8692 (t) cc_final: 0.8335 (m) REVERT: C 603 LEU cc_start: 0.8333 (mt) cc_final: 0.8036 (mm) REVERT: C 615 PHE cc_start: 0.8128 (m-80) cc_final: 0.7398 (m-80) REVERT: C 616 THR cc_start: 0.8477 (t) cc_final: 0.8152 (m) REVERT: C 626 GLU cc_start: 0.6248 (mp0) cc_final: 0.5815 (mp0) REVERT: C 640 ASP cc_start: 0.6704 (t0) cc_final: 0.6491 (t70) REVERT: C 651 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8185 (ttmm) REVERT: C 704 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7193 (mt-10) REVERT: C 772 VAL cc_start: 0.8019 (p) cc_final: 0.7751 (m) REVERT: C 795 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6854 (tm-30) REVERT: C 825 GLN cc_start: 0.8022 (pp30) cc_final: 0.7597 (pp30) REVERT: C 843 LEU cc_start: 0.8114 (tp) cc_final: 0.7876 (tt) REVERT: C 851 MET cc_start: 0.7744 (ttp) cc_final: 0.7541 (ttm) REVERT: C 874 PHE cc_start: 0.8077 (m-80) cc_final: 0.7578 (m-80) REVERT: C 876 ASN cc_start: 0.8220 (m-40) cc_final: 0.7963 (m-40) REVERT: C 957 LEU cc_start: 0.8244 (mt) cc_final: 0.7970 (mp) REVERT: C 979 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7643 (tp40) REVERT: C 1107 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6601 (tm-30) REVERT: C 1120 ASN cc_start: 0.7968 (m-40) cc_final: 0.7577 (m110) REVERT: C 1127 SER cc_start: 0.7973 (t) cc_final: 0.7653 (p) REVERT: C 1156 THR cc_start: 0.8260 (m) cc_final: 0.7802 (p) REVERT: C 1181 THR cc_start: 0.8338 (t) cc_final: 0.8058 (m) REVERT: C 1184 GLU cc_start: 0.7323 (pt0) cc_final: 0.7020 (pm20) REVERT: C 1220 PHE cc_start: 0.7924 (m-80) cc_final: 0.7656 (m-80) outliers start: 74 outliers final: 49 residues processed: 638 average time/residue: 0.1537 time to fit residues: 154.7635 Evaluate side-chains 617 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 563 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 224 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 285 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 298 optimal weight: 0.0170 chunk 106 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 301 GLN A1139 HIS B 814 ASN B1061 GLN B1139 HIS C 40 ASN C 996 GLN ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101501 restraints weight = 40046.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104899 restraints weight = 19271.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107074 restraints weight = 11237.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108537 restraints weight = 7531.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109501 restraints weight = 5632.991| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25014 Z= 0.119 Angle : 0.563 9.708 34131 Z= 0.286 Chirality : 0.043 0.246 4117 Planarity : 0.004 0.041 4250 Dihedral : 6.516 108.152 4385 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.84 % Allowed : 13.84 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 2990 helix: 1.64 (0.21), residues: 627 sheet: -0.31 (0.20), residues: 753 loop : -1.06 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1207 TYR 0.017 0.001 TYR A 606 PHE 0.024 0.001 PHE C 387 TRP 0.008 0.001 TRP C 439 HIS 0.011 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (24918) covalent geometry : angle 0.54589 / 0.28 (33885) SS BOND : bond 0.00387 / 0.24 ( 42) SS BOND : angle 1.93657 / 1.20 ( 84) hydrogen bonds : bond 0.03898 / 2.59 ( 850) hydrogen bonds : angle 5.17224 / 3.51 ( 2583) link_ALPHA1-3 : bond 0.00818 / 0.41 ( 3) link_ALPHA1-3 : angle 1.65709 / 1.20 ( 9) link_ALPHA1-6 : bond 0.00904 / 0.45 ( 3) link_ALPHA1-6 : angle 1.50025 / 1.04 ( 9) link_BETA1-4 : bond 0.00339 / 0.23 ( 12) link_BETA1-4 : angle 1.50444 / 1.09 ( 36) link_NAG-ASN : bond 0.00232 / 0.16 ( 36) link_NAG-ASN : angle 1.65572 / 1.13 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 601 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6405 (m-80) cc_final: 0.6086 (t80) REVERT: A 176 PHE cc_start: 0.7693 (m-80) cc_final: 0.7306 (m-80) REVERT: A 212 TYR cc_start: 0.8076 (m-80) cc_final: 0.7870 (m-10) REVERT: A 213 TYR cc_start: 0.6860 (m-80) cc_final: 0.6296 (m-80) REVERT: A 276 ASN cc_start: 0.7293 (t0) cc_final: 0.6750 (p0) REVERT: A 341 LEU cc_start: 0.8423 (mm) cc_final: 0.8165 (mt) REVERT: A 396 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7668 (mtt180) REVERT: A 444 THR cc_start: 0.7549 (p) cc_final: 0.7288 (p) REVERT: A 470 GLN cc_start: 0.8233 (tt0) cc_final: 0.7916 (tt0) REVERT: A 509 ASP cc_start: 0.7176 (p0) cc_final: 0.6713 (p0) REVERT: A 556 ASN cc_start: 0.5131 (t0) cc_final: 0.4820 (t0) REVERT: A 578 SER cc_start: 0.8484 (m) cc_final: 0.8045 (p) REVERT: A 614 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7517 (ptmm) REVERT: A 615 PHE cc_start: 0.7793 (m-80) cc_final: 0.7585 (m-80) REVERT: A 638 VAL cc_start: 0.8710 (t) cc_final: 0.8424 (p) REVERT: A 644 MET cc_start: 0.7464 (ptp) cc_final: 0.7194 (ptt) REVERT: A 651 LYS cc_start: 0.8380 (tttt) cc_final: 0.7796 (ttpt) REVERT: A 669 SER cc_start: 0.8321 (t) cc_final: 0.7860 (p) REVERT: A 674 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8485 (t) REVERT: A 687 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8300 (tttp) REVERT: A 730 GLU cc_start: 0.7429 (tt0) cc_final: 0.7207 (tt0) REVERT: A 739 ASN cc_start: 0.8031 (m-40) cc_final: 0.7796 (m110) REVERT: A 821 GLN cc_start: 0.7906 (tt0) cc_final: 0.7174 (tm-30) REVERT: A 851 MET cc_start: 0.7530 (ttm) cc_final: 0.7302 (ttp) REVERT: A 856 GLU cc_start: 0.7040 (pm20) cc_final: 0.6497 (pm20) REVERT: A 857 GLU cc_start: 0.7561 (mp0) cc_final: 0.6800 (mp0) REVERT: A 870 ASP cc_start: 0.6264 (t70) cc_final: 0.5930 (t0) REVERT: A 898 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6834 (mm-30) REVERT: A 924 ARG cc_start: 0.7265 (mmp-170) cc_final: 0.7005 (mmt180) REVERT: A 941 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 951 HIS cc_start: 0.7991 (t70) cc_final: 0.7532 (t-90) REVERT: A 954 SER cc_start: 0.8530 (m) cc_final: 0.8261 (p) REVERT: A 1040 GLU cc_start: 0.7318 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 1104 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7756 (mmtp) REVERT: A 1109 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7306 (tp40) REVERT: A 1167 ILE cc_start: 0.7720 (mm) cc_final: 0.7507 (mm) REVERT: A 1211 GLU cc_start: 0.7249 (mp0) cc_final: 0.6901 (mp0) REVERT: A 1230 TYR cc_start: 0.7458 (m-80) cc_final: 0.7138 (m-80) REVERT: B 33 ARG cc_start: 0.4589 (tmt170) cc_final: 0.4167 (tpt-90) REVERT: B 214 MET cc_start: 0.7060 (tpt) cc_final: 0.6759 (tpt) REVERT: B 257 ASN cc_start: 0.7770 (t0) cc_final: 0.7366 (t0) REVERT: B 351 ASN cc_start: 0.7192 (p0) cc_final: 0.6938 (p0) REVERT: B 376 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8209 (mtpp) REVERT: B 509 ASP cc_start: 0.7730 (t0) cc_final: 0.7048 (p0) REVERT: B 593 SER cc_start: 0.8026 (m) cc_final: 0.7557 (p) REVERT: B 648 VAL cc_start: 0.8121 (t) cc_final: 0.7921 (p) REVERT: B 651 LYS cc_start: 0.8208 (tttt) cc_final: 0.7618 (mmmm) REVERT: B 660 GLU cc_start: 0.6642 (mp0) cc_final: 0.6224 (mp0) REVERT: B 668 SER cc_start: 0.8878 (t) cc_final: 0.8496 (p) REVERT: B 670 PHE cc_start: 0.8273 (m-10) cc_final: 0.7660 (m-80) REVERT: B 671 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8209 (mt) REVERT: B 679 ASP cc_start: 0.7508 (m-30) cc_final: 0.7237 (m-30) REVERT: B 740 ASP cc_start: 0.6909 (t0) cc_final: 0.6494 (t0) REVERT: B 757 CYS cc_start: 0.5807 (t) cc_final: 0.5377 (t) REVERT: B 758 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8473 (ttmm) REVERT: B 768 GLN cc_start: 0.7602 (mt0) cc_final: 0.7310 (mt0) REVERT: B 771 GLN cc_start: 0.7805 (pm20) cc_final: 0.7555 (pm20) REVERT: B 796 TYR cc_start: 0.7824 (t80) cc_final: 0.7516 (t80) REVERT: B 820 LYS cc_start: 0.7423 (mttp) cc_final: 0.7074 (mttm) REVERT: B 844 GLU cc_start: 0.7539 (tp30) cc_final: 0.7048 (tp30) REVERT: B 847 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7178 (mt-10) REVERT: B 954 SER cc_start: 0.8280 (m) cc_final: 0.7853 (p) REVERT: B 983 ASN cc_start: 0.7182 (t0) cc_final: 0.6955 (t0) REVERT: B 1039 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: B 1069 ASP cc_start: 0.6905 (t0) cc_final: 0.6514 (t0) REVERT: B 1084 ASP cc_start: 0.7094 (t70) cc_final: 0.6792 (t0) REVERT: B 1107 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7162 (mt-10) REVERT: B 1117 GLN cc_start: 0.7727 (mt0) cc_final: 0.7341 (tt0) REVERT: B 1184 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 1190 PHE cc_start: 0.8390 (p90) cc_final: 0.7753 (p90) REVERT: C 35 PHE cc_start: 0.8434 (t80) cc_final: 0.8141 (t80) REVERT: C 152 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8272 (ptmm) REVERT: C 179 LYS cc_start: 0.7597 (pttp) cc_final: 0.7324 (pttm) REVERT: C 185 PHE cc_start: 0.7978 (t80) cc_final: 0.7673 (t80) REVERT: C 204 MET cc_start: 0.6272 (mtt) cc_final: 0.6015 (mtt) REVERT: C 211 THR cc_start: 0.7910 (m) cc_final: 0.7518 (p) REVERT: C 213 TYR cc_start: 0.7832 (m-80) cc_final: 0.7210 (m-80) REVERT: C 247 ASN cc_start: 0.7958 (p0) cc_final: 0.7395 (p0) REVERT: C 262 LEU cc_start: 0.8038 (mt) cc_final: 0.7837 (mp) REVERT: C 291 TYR cc_start: 0.7457 (m-10) cc_final: 0.7149 (m-10) REVERT: C 354 ASP cc_start: 0.6907 (t0) cc_final: 0.6255 (t0) REVERT: C 387 PHE cc_start: 0.7130 (t80) cc_final: 0.6849 (t80) REVERT: C 456 THR cc_start: 0.7858 (m) cc_final: 0.7646 (m) REVERT: C 463 TYR cc_start: 0.8238 (m-80) cc_final: 0.7963 (m-80) REVERT: C 512 PHE cc_start: 0.6918 (m-80) cc_final: 0.6527 (m-80) REVERT: C 555 TYR cc_start: 0.6535 (m-80) cc_final: 0.6046 (m-80) REVERT: C 569 ASP cc_start: 0.7515 (t70) cc_final: 0.7091 (t0) REVERT: C 581 ASP cc_start: 0.7368 (t0) cc_final: 0.6944 (t0) REVERT: C 590 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8379 (m) REVERT: C 603 LEU cc_start: 0.8315 (mt) cc_final: 0.8054 (mm) REVERT: C 615 PHE cc_start: 0.8094 (m-80) cc_final: 0.7485 (m-80) REVERT: C 616 THR cc_start: 0.8467 (t) cc_final: 0.8124 (m) REVERT: C 626 GLU cc_start: 0.6212 (mp0) cc_final: 0.5833 (mp0) REVERT: C 640 ASP cc_start: 0.6689 (t0) cc_final: 0.6484 (t70) REVERT: C 651 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8167 (ttmt) REVERT: C 704 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6998 (mt-10) REVERT: C 745 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7186 (m) REVERT: C 746 GLU cc_start: 0.7184 (mp0) cc_final: 0.6938 (mp0) REVERT: C 772 VAL cc_start: 0.8022 (p) cc_final: 0.7720 (m) REVERT: C 825 GLN cc_start: 0.8034 (pp30) cc_final: 0.7557 (pp30) REVERT: C 843 LEU cc_start: 0.8149 (tp) cc_final: 0.7943 (tt) REVERT: C 874 PHE cc_start: 0.8023 (m-80) cc_final: 0.7513 (m-80) REVERT: C 876 ASN cc_start: 0.8141 (m-40) cc_final: 0.7862 (m-40) REVERT: C 898 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 957 LEU cc_start: 0.8251 (mt) cc_final: 0.7935 (mp) REVERT: C 979 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7517 (tp40) REVERT: C 1107 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: C 1120 ASN cc_start: 0.7946 (m-40) cc_final: 0.7552 (m110) REVERT: C 1127 SER cc_start: 0.7990 (t) cc_final: 0.7681 (p) REVERT: C 1181 THR cc_start: 0.8367 (t) cc_final: 0.8082 (m) REVERT: C 1220 PHE cc_start: 0.7930 (m-80) cc_final: 0.7635 (m-80) outliers start: 76 outliers final: 51 residues processed: 630 average time/residue: 0.1528 time to fit residues: 152.4267 Evaluate side-chains 632 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 573 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 ASN A 258 ASN A 301 GLN A 814 ASN A1109 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN C 40 ASN C 996 GLN ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100509 restraints weight = 39849.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103950 restraints weight = 19089.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105824 restraints weight = 11091.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107499 restraints weight = 7830.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108521 restraints weight = 5708.535| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25014 Z= 0.164 Angle : 0.585 14.988 34131 Z= 0.299 Chirality : 0.044 0.256 4117 Planarity : 0.004 0.048 4250 Dihedral : 6.599 108.540 4385 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.59 % Allowed : 14.40 % Favored : 82.01 % 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 (0.15), residues: 2990 helix: 1.67 (0.21), residues: 626 sheet: -0.33 (0.20), residues: 754 loop : -1.06 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.019 0.001 TYR A 606 PHE 0.023 0.001 PHE C 387 TRP 0.017 0.001 TRP C 168 HIS 0.018 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (24918) covalent geometry : angle 0.56493 / 0.29 (33885) SS BOND : bond 0.00420 / 0.26 ( 42) SS BOND : angle 2.18217 / 1.37 ( 84) hydrogen bonds : bond 0.04044 / 2.68 ( 850) hydrogen bonds : angle 5.09334 / 3.45 ( 2583) link_ALPHA1-3 : bond 0.00764 / 0.39 ( 3) link_ALPHA1-3 : angle 1.81432 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00863 / 0.43 ( 3) link_ALPHA1-6 : angle 1.53072 / 1.05 ( 9) link_BETA1-4 : bond 0.00333 / 0.22 ( 12) link_BETA1-4 : angle 1.54324 / 1.11 ( 36) link_NAG-ASN : bond 0.00211 / 0.13 ( 36) link_NAG-ASN : angle 1.75925 / 1.21 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 581 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6418 (m-80) cc_final: 0.5936 (t80) REVERT: A 176 PHE cc_start: 0.7812 (m-80) cc_final: 0.7367 (m-80) REVERT: A 213 TYR cc_start: 0.6910 (m-80) cc_final: 0.6233 (m-80) REVERT: A 227 TYR cc_start: 0.7130 (p90) cc_final: 0.6626 (p90) REVERT: A 276 ASN cc_start: 0.7307 (t0) cc_final: 0.6825 (p0) REVERT: A 341 LEU cc_start: 0.8538 (mm) cc_final: 0.8312 (mt) REVERT: A 396 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7818 (mtt180) REVERT: A 444 THR cc_start: 0.7471 (p) cc_final: 0.7257 (p) REVERT: A 470 GLN cc_start: 0.8141 (tt0) cc_final: 0.7850 (tt0) REVERT: A 509 ASP cc_start: 0.7316 (p0) cc_final: 0.6735 (p0) REVERT: A 556 ASN cc_start: 0.4936 (t0) cc_final: 0.4323 (t0) REVERT: A 578 SER cc_start: 0.8463 (m) cc_final: 0.7958 (p) REVERT: A 615 PHE cc_start: 0.7848 (m-80) cc_final: 0.7640 (m-80) REVERT: A 624 LYS cc_start: 0.7402 (tppp) cc_final: 0.7168 (tppp) REVERT: A 651 LYS cc_start: 0.8398 (tttt) cc_final: 0.7739 (ttpt) REVERT: A 669 SER cc_start: 0.8330 (t) cc_final: 0.7850 (p) REVERT: A 674 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8490 (t) REVERT: A 687 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8248 (tttp) REVERT: A 728 THR cc_start: 0.8022 (t) cc_final: 0.7745 (p) REVERT: A 730 GLU cc_start: 0.7509 (tt0) cc_final: 0.7258 (tt0) REVERT: A 821 GLN cc_start: 0.8022 (tt0) cc_final: 0.7197 (tm-30) REVERT: A 856 GLU cc_start: 0.7172 (pm20) cc_final: 0.6563 (pm20) REVERT: A 857 GLU cc_start: 0.7729 (mp0) cc_final: 0.6862 (mp0) REVERT: A 870 ASP cc_start: 0.6401 (t70) cc_final: 0.6067 (t0) REVERT: A 924 ARG cc_start: 0.7391 (mmp-170) cc_final: 0.7096 (mmt180) REVERT: A 948 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 951 HIS cc_start: 0.7939 (t70) cc_final: 0.7474 (t-90) REVERT: A 954 SER cc_start: 0.8553 (m) cc_final: 0.8277 (p) REVERT: A 1040 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6885 (tm-30) REVERT: A 1104 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7681 (mmtp) REVERT: A 1121 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6555 (mm-30) REVERT: A 1167 ILE cc_start: 0.7714 (mm) cc_final: 0.7478 (mm) REVERT: A 1211 GLU cc_start: 0.7325 (mp0) cc_final: 0.6995 (mp0) REVERT: A 1230 TYR cc_start: 0.7538 (m-80) cc_final: 0.6992 (m-80) REVERT: B 214 MET cc_start: 0.7103 (tpt) cc_final: 0.6801 (tpt) REVERT: B 257 ASN cc_start: 0.7861 (t0) cc_final: 0.7408 (t0) REVERT: B 272 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8334 (mtpp) REVERT: B 285 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8327 (pp) REVERT: B 351 ASN cc_start: 0.7229 (p0) cc_final: 0.6905 (p0) REVERT: B 372 TYR cc_start: 0.6553 (m-10) cc_final: 0.6249 (m-80) REVERT: B 438 PHE cc_start: 0.8634 (m-80) cc_final: 0.8397 (m-80) REVERT: B 507 PHE cc_start: 0.7975 (p90) cc_final: 0.7738 (p90) REVERT: B 509 ASP cc_start: 0.7736 (t0) cc_final: 0.6770 (p0) REVERT: B 593 SER cc_start: 0.8075 (m) cc_final: 0.7544 (p) REVERT: B 651 LYS cc_start: 0.8189 (tttt) cc_final: 0.7544 (mmmm) REVERT: B 660 GLU cc_start: 0.6688 (mp0) cc_final: 0.6259 (mp0) REVERT: B 668 SER cc_start: 0.8895 (t) cc_final: 0.8503 (p) REVERT: B 670 PHE cc_start: 0.8305 (m-10) cc_final: 0.7612 (m-80) REVERT: B 679 ASP cc_start: 0.7725 (m-30) cc_final: 0.7476 (m-30) REVERT: B 740 ASP cc_start: 0.6941 (t0) cc_final: 0.6456 (t0) REVERT: B 757 CYS cc_start: 0.5910 (t) cc_final: 0.5491 (t) REVERT: B 758 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8336 (ttmm) REVERT: B 768 GLN cc_start: 0.7652 (mt0) cc_final: 0.7361 (mt0) REVERT: B 771 GLN cc_start: 0.7913 (pm20) cc_final: 0.7522 (pm20) REVERT: B 795 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: B 796 TYR cc_start: 0.7825 (t80) cc_final: 0.7503 (t80) REVERT: B 820 LYS cc_start: 0.7311 (mttp) cc_final: 0.7036 (tppt) REVERT: B 844 GLU cc_start: 0.7556 (tp30) cc_final: 0.7117 (tp30) REVERT: B 847 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7259 (mt-10) REVERT: B 945 VAL cc_start: 0.8493 (p) cc_final: 0.8225 (m) REVERT: B 954 SER cc_start: 0.8318 (m) cc_final: 0.7898 (p) REVERT: B 983 ASN cc_start: 0.7301 (t0) cc_final: 0.7051 (t0) REVERT: B 1069 ASP cc_start: 0.7097 (t0) cc_final: 0.6809 (t0) REVERT: B 1084 ASP cc_start: 0.7278 (t70) cc_final: 0.6933 (t0) REVERT: B 1107 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 1117 GLN cc_start: 0.7668 (mt0) cc_final: 0.7309 (tt0) REVERT: B 1184 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 1227 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7661 (t) REVERT: C 35 PHE cc_start: 0.8435 (t80) cc_final: 0.7968 (t80) REVERT: C 152 LYS cc_start: 0.8915 (ptmt) cc_final: 0.8279 (ptmm) REVERT: C 176 PHE cc_start: 0.7764 (m-80) cc_final: 0.7497 (m-10) REVERT: C 179 LYS cc_start: 0.7690 (pttp) cc_final: 0.7476 (pttm) REVERT: C 185 PHE cc_start: 0.7989 (t80) cc_final: 0.7612 (t80) REVERT: C 204 MET cc_start: 0.6445 (mtt) cc_final: 0.6123 (mtt) REVERT: C 211 THR cc_start: 0.7893 (m) cc_final: 0.7468 (p) REVERT: C 213 TYR cc_start: 0.7845 (m-80) cc_final: 0.7279 (m-80) REVERT: C 247 ASN cc_start: 0.7874 (p0) cc_final: 0.7333 (p0) REVERT: C 291 TYR cc_start: 0.7429 (m-10) cc_final: 0.7123 (m-10) REVERT: C 354 ASP cc_start: 0.7014 (t0) cc_final: 0.6343 (t0) REVERT: C 463 TYR cc_start: 0.8207 (m-80) cc_final: 0.7913 (m-80) REVERT: C 512 PHE cc_start: 0.6888 (m-80) cc_final: 0.6447 (m-80) REVERT: C 555 TYR cc_start: 0.6640 (m-80) cc_final: 0.6253 (m-80) REVERT: C 566 ASN cc_start: 0.7942 (t0) cc_final: 0.7540 (t0) REVERT: C 569 ASP cc_start: 0.7492 (t70) cc_final: 0.7055 (t0) REVERT: C 581 ASP cc_start: 0.7490 (t0) cc_final: 0.6975 (t0) REVERT: C 590 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8319 (m) REVERT: C 615 PHE cc_start: 0.8077 (m-80) cc_final: 0.7764 (m-80) REVERT: C 616 THR cc_start: 0.8473 (t) cc_final: 0.8158 (m) REVERT: C 624 LYS cc_start: 0.7816 (tppt) cc_final: 0.7432 (tppt) REVERT: C 626 GLU cc_start: 0.6282 (mp0) cc_final: 0.5873 (mp0) REVERT: C 640 ASP cc_start: 0.6806 (t0) cc_final: 0.6522 (t70) REVERT: C 651 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7825 (ttmm) REVERT: C 660 GLU cc_start: 0.7579 (mp0) cc_final: 0.7338 (mp0) REVERT: C 704 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7098 (mt-10) REVERT: C 745 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7271 (m) REVERT: C 746 GLU cc_start: 0.7240 (mp0) cc_final: 0.6960 (mp0) REVERT: C 772 VAL cc_start: 0.8044 (p) cc_final: 0.7747 (m) REVERT: C 825 GLN cc_start: 0.8076 (pp30) cc_final: 0.7475 (pp30) REVERT: C 843 LEU cc_start: 0.8047 (tp) cc_final: 0.7842 (tt) REVERT: C 851 MET cc_start: 0.7852 (ttp) cc_final: 0.7629 (ttm) REVERT: C 874 PHE cc_start: 0.8144 (m-80) cc_final: 0.7632 (m-80) REVERT: C 876 ASN cc_start: 0.8184 (m-40) cc_final: 0.7934 (m-40) REVERT: C 898 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7612 (mt-10) REVERT: C 957 LEU cc_start: 0.8210 (mt) cc_final: 0.7933 (mp) REVERT: C 979 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7538 (tp40) REVERT: C 1107 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: C 1120 ASN cc_start: 0.7923 (m-40) cc_final: 0.7576 (m110) REVERT: C 1127 SER cc_start: 0.7974 (t) cc_final: 0.7679 (p) REVERT: C 1184 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: C 1220 PHE cc_start: 0.7929 (m-80) cc_final: 0.7545 (m-80) outliers start: 96 outliers final: 70 residues processed: 625 average time/residue: 0.1558 time to fit residues: 154.9614 Evaluate side-chains 639 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 561 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain B residue 1227 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 954 SER Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 185 optimal weight: 2.9990 chunk 235 optimal weight: 0.0970 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 301 GLN A 739 ASN A 814 ASN A1043 ASN A1120 ASN A1139 HIS ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN C 40 ASN C 59 GLN C 170 ASN C 996 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099160 restraints weight = 40139.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102591 restraints weight = 19234.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104751 restraints weight = 11176.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106239 restraints weight = 7556.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107056 restraints weight = 5615.091| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25014 Z= 0.183 Angle : 0.605 15.766 34131 Z= 0.308 Chirality : 0.044 0.267 4117 Planarity : 0.004 0.049 4250 Dihedral : 6.752 108.844 4385 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.12 % Allowed : 15.23 % Favored : 80.66 % 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: -0.46 (0.15), residues: 2990 helix: 1.56 (0.20), residues: 636 sheet: -0.34 (0.20), residues: 724 loop : -1.05 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1207 TYR 0.019 0.002 TYR C 227 PHE 0.023 0.002 PHE A 507 TRP 0.009 0.001 TRP C 259 HIS 0.013 0.001 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (24918) covalent geometry : angle 0.58428 / 0.30 (33885) SS BOND : bond 0.00525 / 0.34 ( 42) SS BOND : angle 2.21490 / 1.40 ( 84) hydrogen bonds : bond 0.04148 / 2.75 ( 850) hydrogen bonds : angle 5.03707 / 3.42 ( 2583) link_ALPHA1-3 : bond 0.00841 / 0.42 ( 3) link_ALPHA1-3 : angle 1.83300 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00970 / 0.49 ( 3) link_ALPHA1-6 : angle 1.57433 / 1.07 ( 9) link_BETA1-4 : bond 0.00342 / 0.22 ( 12) link_BETA1-4 : angle 1.65723 / 1.19 ( 36) link_NAG-ASN : bond 0.00277 / 0.18 ( 36) link_NAG-ASN : angle 1.87697 / 1.29 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 582 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6400 (m-80) cc_final: 0.5917 (t80) REVERT: A 176 PHE cc_start: 0.7892 (m-80) cc_final: 0.7418 (m-80) REVERT: A 213 TYR cc_start: 0.6937 (m-80) cc_final: 0.6236 (m-80) REVERT: A 276 ASN cc_start: 0.7345 (t0) cc_final: 0.6807 (p0) REVERT: A 396 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7802 (mtt180) REVERT: A 444 THR cc_start: 0.7492 (p) cc_final: 0.7285 (p) REVERT: A 470 GLN cc_start: 0.8140 (tt0) cc_final: 0.7848 (tt0) REVERT: A 482 ASP cc_start: 0.6921 (p0) cc_final: 0.6620 (p0) REVERT: A 509 ASP cc_start: 0.7359 (p0) cc_final: 0.6992 (p0) REVERT: A 556 ASN cc_start: 0.4967 (t0) cc_final: 0.4496 (t0) REVERT: A 578 SER cc_start: 0.8455 (m) cc_final: 0.7926 (p) REVERT: A 615 PHE cc_start: 0.7890 (m-80) cc_final: 0.7664 (m-80) REVERT: A 624 LYS cc_start: 0.7498 (tppp) cc_final: 0.7238 (tppp) REVERT: A 651 LYS cc_start: 0.8378 (tttt) cc_final: 0.7728 (ttpt) REVERT: A 669 SER cc_start: 0.8270 (t) cc_final: 0.7844 (p) REVERT: A 674 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8518 (t) REVERT: A 687 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8221 (tttp) REVERT: A 704 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6237 (mt-10) REVERT: A 728 THR cc_start: 0.8094 (t) cc_final: 0.7879 (p) REVERT: A 730 GLU cc_start: 0.7459 (tt0) cc_final: 0.7213 (tt0) REVERT: A 821 GLN cc_start: 0.7976 (tt0) cc_final: 0.7163 (tm-30) REVERT: A 856 GLU cc_start: 0.7192 (pm20) cc_final: 0.6582 (pm20) REVERT: A 857 GLU cc_start: 0.7707 (mp0) cc_final: 0.6597 (mp0) REVERT: A 870 ASP cc_start: 0.6431 (t70) cc_final: 0.6129 (t0) REVERT: A 924 ARG cc_start: 0.7408 (mmp-170) cc_final: 0.7106 (mmt180) REVERT: A 948 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6718 (tm-30) REVERT: A 951 HIS cc_start: 0.7910 (t70) cc_final: 0.7467 (t-90) REVERT: A 954 SER cc_start: 0.8626 (m) cc_final: 0.8307 (p) REVERT: A 1104 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7667 (mmtp) REVERT: A 1107 GLU cc_start: 0.7456 (tp30) cc_final: 0.7234 (tp30) REVERT: A 1109 GLN cc_start: 0.7786 (tp40) cc_final: 0.7376 (tp40) REVERT: A 1121 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 1167 ILE cc_start: 0.7674 (mm) cc_final: 0.7448 (mm) REVERT: A 1211 GLU cc_start: 0.7247 (mp0) cc_final: 0.6967 (mp0) REVERT: A 1230 TYR cc_start: 0.7607 (m-10) cc_final: 0.7060 (m-80) REVERT: B 46 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7222 (m) REVERT: B 214 MET cc_start: 0.7084 (tpt) cc_final: 0.6742 (tpt) REVERT: B 257 ASN cc_start: 0.7869 (t0) cc_final: 0.7441 (t0) REVERT: B 351 ASN cc_start: 0.7202 (p0) cc_final: 0.6900 (p0) REVERT: B 372 TYR cc_start: 0.6504 (m-10) cc_final: 0.6206 (m-80) REVERT: B 438 PHE cc_start: 0.8650 (m-80) cc_final: 0.8394 (m-10) REVERT: B 507 PHE cc_start: 0.7935 (p90) cc_final: 0.7729 (p90) REVERT: B 509 ASP cc_start: 0.7694 (t0) cc_final: 0.6666 (p0) REVERT: B 593 SER cc_start: 0.8095 (m) cc_final: 0.7597 (p) REVERT: B 651 LYS cc_start: 0.8184 (tttt) cc_final: 0.7529 (mmmm) REVERT: B 660 GLU cc_start: 0.6713 (mp0) cc_final: 0.6352 (mp0) REVERT: B 668 SER cc_start: 0.8899 (t) cc_final: 0.8493 (p) REVERT: B 670 PHE cc_start: 0.8317 (m-10) cc_final: 0.7614 (m-80) REVERT: B 679 ASP cc_start: 0.7752 (m-30) cc_final: 0.7512 (m-30) REVERT: B 740 ASP cc_start: 0.6826 (t0) cc_final: 0.6396 (t0) REVERT: B 757 CYS cc_start: 0.5923 (t) cc_final: 0.5503 (t) REVERT: B 758 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8323 (ttmm) REVERT: B 768 GLN cc_start: 0.7681 (mt0) cc_final: 0.7363 (mt0) REVERT: B 771 GLN cc_start: 0.7957 (pm20) cc_final: 0.7530 (pm20) REVERT: B 795 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: B 796 TYR cc_start: 0.7862 (t80) cc_final: 0.7553 (t80) REVERT: B 820 LYS cc_start: 0.7314 (mttp) cc_final: 0.7058 (tppt) REVERT: B 844 GLU cc_start: 0.7560 (tp30) cc_final: 0.7115 (tp30) REVERT: B 847 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 945 VAL cc_start: 0.8515 (p) cc_final: 0.8258 (m) REVERT: B 954 SER cc_start: 0.8339 (m) cc_final: 0.7923 (p) REVERT: B 983 ASN cc_start: 0.7321 (t0) cc_final: 0.7076 (t0) REVERT: B 1069 ASP cc_start: 0.7103 (t0) cc_final: 0.6785 (t0) REVERT: B 1084 ASP cc_start: 0.7320 (t70) cc_final: 0.6956 (t0) REVERT: B 1107 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7238 (mt-10) REVERT: B 1111 SER cc_start: 0.8116 (t) cc_final: 0.7845 (p) REVERT: B 1117 GLN cc_start: 0.7709 (mt0) cc_final: 0.7306 (tt0) REVERT: B 1138 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 1184 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7130 (mm-30) REVERT: C 35 PHE cc_start: 0.8427 (t80) cc_final: 0.8094 (t80) REVERT: C 152 LYS cc_start: 0.8946 (ptmt) cc_final: 0.8279 (ptmm) REVERT: C 179 LYS cc_start: 0.7687 (pttp) cc_final: 0.7449 (pttm) REVERT: C 185 PHE cc_start: 0.8079 (t80) cc_final: 0.7630 (t80) REVERT: C 204 MET cc_start: 0.6529 (mtt) cc_final: 0.6268 (mtt) REVERT: C 211 THR cc_start: 0.7897 (m) cc_final: 0.7556 (p) REVERT: C 213 TYR cc_start: 0.7881 (m-80) cc_final: 0.7357 (m-80) REVERT: C 247 ASN cc_start: 0.7826 (p0) cc_final: 0.7359 (p0) REVERT: C 291 TYR cc_start: 0.7435 (m-10) cc_final: 0.7094 (m-10) REVERT: C 354 ASP cc_start: 0.7096 (t0) cc_final: 0.6433 (t0) REVERT: C 387 PHE cc_start: 0.6920 (t80) cc_final: 0.6690 (t80) REVERT: C 463 TYR cc_start: 0.8248 (m-80) cc_final: 0.7911 (m-80) REVERT: C 507 PHE cc_start: 0.8399 (p90) cc_final: 0.8056 (p90) REVERT: C 512 PHE cc_start: 0.6878 (m-80) cc_final: 0.6415 (m-80) REVERT: C 555 TYR cc_start: 0.6800 (m-80) cc_final: 0.6371 (m-80) REVERT: C 566 ASN cc_start: 0.7948 (t0) cc_final: 0.7563 (t0) REVERT: C 569 ASP cc_start: 0.7509 (t70) cc_final: 0.7097 (t0) REVERT: C 581 ASP cc_start: 0.7512 (t0) cc_final: 0.6872 (t0) REVERT: C 590 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8294 (m) REVERT: C 615 PHE cc_start: 0.8040 (m-80) cc_final: 0.7812 (m-80) REVERT: C 616 THR cc_start: 0.8406 (t) cc_final: 0.8158 (m) REVERT: C 624 LYS cc_start: 0.7904 (tppt) cc_final: 0.7558 (tppt) REVERT: C 626 GLU cc_start: 0.6298 (mp0) cc_final: 0.5879 (mp0) REVERT: C 633 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7849 (ptmm) REVERT: C 640 ASP cc_start: 0.6827 (t0) cc_final: 0.6544 (t70) REVERT: C 651 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7929 (ttmt) REVERT: C 745 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7677 (m) REVERT: C 772 VAL cc_start: 0.8072 (p) cc_final: 0.7775 (m) REVERT: C 801 ASN cc_start: 0.7971 (p0) cc_final: 0.7658 (p0) REVERT: C 825 GLN cc_start: 0.8086 (pp30) cc_final: 0.7749 (pp30) REVERT: C 843 LEU cc_start: 0.8031 (tp) cc_final: 0.7814 (tt) REVERT: C 874 PHE cc_start: 0.8172 (m-80) cc_final: 0.7655 (m-80) REVERT: C 876 ASN cc_start: 0.8181 (m-40) cc_final: 0.7974 (m-40) REVERT: C 898 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 957 LEU cc_start: 0.8234 (mt) cc_final: 0.7916 (mp) REVERT: C 966 PHE cc_start: 0.7310 (t80) cc_final: 0.7011 (t80) REVERT: C 979 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7575 (tp40) REVERT: C 1107 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: C 1120 ASN cc_start: 0.7964 (m-40) cc_final: 0.7561 (m-40) REVERT: C 1127 SER cc_start: 0.7984 (t) cc_final: 0.7678 (p) REVERT: C 1220 PHE cc_start: 0.7969 (m-80) cc_final: 0.7540 (m-80) outliers start: 110 outliers final: 89 residues processed: 636 average time/residue: 0.1729 time to fit residues: 174.1986 Evaluate side-chains 655 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 560 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 700 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 482 ASP Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 814 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 954 SER Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 139 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 508 ASN A 739 ASN A1139 HIS ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN C 40 ASN C 996 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104750 restraints weight = 39056.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108146 restraints weight = 18797.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110346 restraints weight = 10985.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111757 restraints weight = 7378.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112637 restraints weight = 5551.024| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25014 Z= 0.117 Angle : 0.582 14.723 34131 Z= 0.293 Chirality : 0.044 0.253 4117 Planarity : 0.004 0.048 4250 Dihedral : 6.537 106.716 4385 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.37 % Allowed : 16.65 % Favored : 79.99 % 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: -0.35 (0.15), residues: 2990 helix: 1.77 (0.21), residues: 635 sheet: -0.34 (0.20), residues: 720 loop : -1.00 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1235 TYR 0.017 0.001 TYR A 953 PHE 0.032 0.001 PHE A 387 TRP 0.019 0.001 TRP C 168 HIS 0.012 0.001 HIS B1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (24918) covalent geometry : angle 0.56101 / 0.29 (33885) SS BOND : bond 0.00489 / 0.33 ( 42) SS BOND : angle 2.09088 / 1.33 ( 84) hydrogen bonds : bond 0.03652 / 2.41 ( 850) hydrogen bonds : angle 4.84677 / 3.29 ( 2583) link_ALPHA1-3 : bond 0.00881 / 0.44 ( 3) link_ALPHA1-3 : angle 1.68636 / 1.19 ( 9) link_ALPHA1-6 : bond 0.01116 / 0.56 ( 3) link_ALPHA1-6 : angle 1.59704 / 1.12 ( 9) link_BETA1-4 : bond 0.00352 / 0.24 ( 12) link_BETA1-4 : angle 1.46995 / 1.06 ( 36) link_NAG-ASN : bond 0.00178 / 0.12 ( 36) link_NAG-ASN : angle 1.88468 / 1.31 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 578 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 PHE cc_start: 0.7885 (m-80) cc_final: 0.7405 (m-80) REVERT: A 213 TYR cc_start: 0.6934 (m-80) cc_final: 0.6239 (m-80) REVERT: A 227 TYR cc_start: 0.7091 (p90) cc_final: 0.6620 (p90) REVERT: A 276 ASN cc_start: 0.7285 (t0) cc_final: 0.6794 (p0) REVERT: A 280 LEU cc_start: 0.8272 (tp) cc_final: 0.8054 (tp) REVERT: A 396 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7575 (mtt180) REVERT: A 509 ASP cc_start: 0.7362 (p0) cc_final: 0.7014 (p0) REVERT: A 556 ASN cc_start: 0.5093 (t0) cc_final: 0.4851 (t0) REVERT: A 578 SER cc_start: 0.8438 (m) cc_final: 0.7914 (p) REVERT: A 614 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7462 (ptmm) REVERT: A 615 PHE cc_start: 0.7873 (m-80) cc_final: 0.7631 (m-80) REVERT: A 624 LYS cc_start: 0.7548 (tppp) cc_final: 0.7280 (tppp) REVERT: A 651 LYS cc_start: 0.8384 (tttt) cc_final: 0.7753 (ttpt) REVERT: A 669 SER cc_start: 0.8294 (t) cc_final: 0.7865 (p) REVERT: A 674 VAL cc_start: 0.8794 (m) cc_final: 0.8475 (t) REVERT: A 680 SER cc_start: 0.8758 (p) cc_final: 0.8279 (m) REVERT: A 687 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8245 (tttp) REVERT: A 704 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6196 (mt-10) REVERT: A 728 THR cc_start: 0.8108 (t) cc_final: 0.7889 (p) REVERT: A 730 GLU cc_start: 0.7485 (tt0) cc_final: 0.7246 (tt0) REVERT: A 814 ASN cc_start: 0.8708 (t0) cc_final: 0.8332 (t0) REVERT: A 821 GLN cc_start: 0.7937 (tt0) cc_final: 0.7116 (tm-30) REVERT: A 856 GLU cc_start: 0.7123 (pm20) cc_final: 0.6541 (pm20) REVERT: A 857 GLU cc_start: 0.7671 (mp0) cc_final: 0.6587 (mp0) REVERT: A 870 ASP cc_start: 0.6378 (t70) cc_final: 0.6059 (t0) REVERT: A 924 ARG cc_start: 0.7380 (mmp-170) cc_final: 0.7102 (mmt180) REVERT: A 941 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 948 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6735 (tm-30) REVERT: A 951 HIS cc_start: 0.7873 (t70) cc_final: 0.7459 (t-90) REVERT: A 954 SER cc_start: 0.8618 (m) cc_final: 0.8232 (p) REVERT: A 1040 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7146 (tm-30) REVERT: A 1104 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7635 (mmtp) REVERT: A 1109 GLN cc_start: 0.7604 (tp40) cc_final: 0.7172 (tp40) REVERT: A 1211 GLU cc_start: 0.7072 (mp0) cc_final: 0.6797 (mp0) REVERT: A 1230 TYR cc_start: 0.7532 (m-10) cc_final: 0.7026 (m-80) REVERT: B 46 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7238 (m) REVERT: B 214 MET cc_start: 0.7066 (tpt) cc_final: 0.6735 (tpt) REVERT: B 225 ILE cc_start: 0.8420 (mt) cc_final: 0.8093 (tp) REVERT: B 237 TYR cc_start: 0.8289 (t80) cc_final: 0.8055 (t80) REVERT: B 257 ASN cc_start: 0.7849 (t0) cc_final: 0.7393 (t0) REVERT: B 351 ASN cc_start: 0.7197 (p0) cc_final: 0.6864 (p0) REVERT: B 372 TYR cc_start: 0.6336 (m-10) cc_final: 0.5798 (m-10) REVERT: B 438 PHE cc_start: 0.8611 (m-80) cc_final: 0.8356 (m-10) REVERT: B 444 THR cc_start: 0.8141 (p) cc_final: 0.7834 (p) REVERT: B 509 ASP cc_start: 0.7743 (t0) cc_final: 0.6987 (p0) REVERT: B 593 SER cc_start: 0.8144 (m) cc_final: 0.7612 (p) REVERT: B 651 LYS cc_start: 0.8219 (tttt) cc_final: 0.7567 (mmmm) REVERT: B 660 GLU cc_start: 0.6693 (mp0) cc_final: 0.6368 (mp0) REVERT: B 668 SER cc_start: 0.8823 (t) cc_final: 0.8483 (p) REVERT: B 670 PHE cc_start: 0.8355 (m-10) cc_final: 0.7653 (m-80) REVERT: B 679 ASP cc_start: 0.7717 (m-30) cc_final: 0.7481 (m-30) REVERT: B 740 ASP cc_start: 0.6911 (t0) cc_final: 0.6442 (t0) REVERT: B 757 CYS cc_start: 0.5865 (t) cc_final: 0.5460 (t) REVERT: B 758 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8331 (ttmm) REVERT: B 768 GLN cc_start: 0.7636 (mt0) cc_final: 0.7324 (mt0) REVERT: B 771 GLN cc_start: 0.7931 (pm20) cc_final: 0.7511 (pm20) REVERT: B 795 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: B 844 GLU cc_start: 0.7523 (tp30) cc_final: 0.7044 (tp30) REVERT: B 847 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7243 (mt-10) REVERT: B 945 VAL cc_start: 0.8459 (p) cc_final: 0.8188 (m) REVERT: B 954 SER cc_start: 0.8294 (m) cc_final: 0.7872 (p) REVERT: B 1069 ASP cc_start: 0.7092 (t0) cc_final: 0.6763 (t0) REVERT: B 1084 ASP cc_start: 0.7143 (t70) cc_final: 0.6809 (t0) REVERT: B 1107 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 1117 GLN cc_start: 0.7626 (mt0) cc_final: 0.7363 (tt0) REVERT: B 1138 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 1184 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7085 (mm-30) REVERT: C 35 PHE cc_start: 0.8453 (t80) cc_final: 0.7946 (t80) REVERT: C 152 LYS cc_start: 0.8900 (ptmt) cc_final: 0.8355 (ptmm) REVERT: C 176 PHE cc_start: 0.7778 (m-80) cc_final: 0.7484 (m-10) REVERT: C 179 LYS cc_start: 0.7670 (pttp) cc_final: 0.7439 (pttm) REVERT: C 185 PHE cc_start: 0.8048 (t80) cc_final: 0.7639 (t80) REVERT: C 204 MET cc_start: 0.6452 (mtt) cc_final: 0.6223 (mtt) REVERT: C 211 THR cc_start: 0.7878 (m) cc_final: 0.7562 (p) REVERT: C 213 TYR cc_start: 0.7992 (m-80) cc_final: 0.7473 (m-80) REVERT: C 247 ASN cc_start: 0.7842 (p0) cc_final: 0.7346 (p0) REVERT: C 291 TYR cc_start: 0.7408 (m-10) cc_final: 0.7133 (m-10) REVERT: C 317 GLU cc_start: 0.7088 (tp30) cc_final: 0.6526 (tp30) REVERT: C 354 ASP cc_start: 0.7063 (t0) cc_final: 0.6438 (t0) REVERT: C 456 THR cc_start: 0.7900 (m) cc_final: 0.7675 (m) REVERT: C 460 ARG cc_start: 0.7658 (ptm160) cc_final: 0.7434 (ptm160) REVERT: C 463 TYR cc_start: 0.8231 (m-80) cc_final: 0.7897 (m-80) REVERT: C 512 PHE cc_start: 0.6660 (m-80) cc_final: 0.6260 (m-80) REVERT: C 555 TYR cc_start: 0.6754 (m-80) cc_final: 0.6325 (m-80) REVERT: C 566 ASN cc_start: 0.7985 (t0) cc_final: 0.7577 (t0) REVERT: C 569 ASP cc_start: 0.7506 (t70) cc_final: 0.7106 (t0) REVERT: C 581 ASP cc_start: 0.7451 (t0) cc_final: 0.6960 (t0) REVERT: C 590 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8323 (m) REVERT: C 615 PHE cc_start: 0.8040 (m-80) cc_final: 0.7837 (m-80) REVERT: C 616 THR cc_start: 0.8368 (t) cc_final: 0.8094 (m) REVERT: C 624 LYS cc_start: 0.7858 (tppt) cc_final: 0.7579 (tppt) REVERT: C 626 GLU cc_start: 0.6246 (mp0) cc_final: 0.5852 (mp0) REVERT: C 633 LYS cc_start: 0.8114 (ptmm) cc_final: 0.7821 (ptmm) REVERT: C 640 ASP cc_start: 0.6916 (t0) cc_final: 0.6614 (t70) REVERT: C 651 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8007 (ttmt) REVERT: C 745 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 825 GLN cc_start: 0.8084 (pp30) cc_final: 0.7757 (pp30) REVERT: C 843 LEU cc_start: 0.8031 (tp) cc_final: 0.7825 (tt) REVERT: C 857 GLU cc_start: 0.7236 (tp30) cc_final: 0.6846 (tp30) REVERT: C 874 PHE cc_start: 0.8131 (m-80) cc_final: 0.7550 (m-80) REVERT: C 876 ASN cc_start: 0.8120 (m-40) cc_final: 0.7895 (m-40) REVERT: C 957 LEU cc_start: 0.8201 (mt) cc_final: 0.7872 (mp) REVERT: C 966 PHE cc_start: 0.7178 (t80) cc_final: 0.6962 (t80) REVERT: C 979 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7574 (tp40) REVERT: C 1001 GLU cc_start: 0.7651 (tp30) cc_final: 0.7002 (tp30) REVERT: C 1061 GLN cc_start: 0.7653 (mp10) cc_final: 0.7241 (pm20) REVERT: C 1107 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6703 (tm-30) REVERT: C 1120 ASN cc_start: 0.7856 (m-40) cc_final: 0.7443 (m-40) REVERT: C 1127 SER cc_start: 0.7936 (t) cc_final: 0.7631 (p) REVERT: C 1220 PHE cc_start: 0.7975 (m-80) cc_final: 0.7533 (m-80) outliers start: 90 outliers final: 67 residues processed: 620 average time/residue: 0.1644 time to fit residues: 161.8062 Evaluate side-chains 627 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 554 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 270 HIS Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 18 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 144 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 270 HIS A 301 GLN A 508 ASN A 621 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN C 40 ASN C 996 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106719 restraints weight = 39060.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110188 restraints weight = 18678.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112400 restraints weight = 10826.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113723 restraints weight = 7261.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114683 restraints weight = 5508.621| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25014 Z= 0.135 Angle : 0.607 14.459 34131 Z= 0.306 Chirality : 0.044 0.246 4117 Planarity : 0.004 0.052 4250 Dihedral : 6.556 104.776 4385 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.48 % Allowed : 16.95 % Favored : 79.57 % 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: -0.33 (0.15), residues: 2990 helix: 1.83 (0.21), residues: 630 sheet: -0.26 (0.20), residues: 693 loop : -1.03 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1235 TYR 0.023 0.001 TYR C 227 PHE 0.037 0.001 PHE A 387 TRP 0.014 0.001 TRP C 168 HIS 0.015 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (24918) covalent geometry : angle 0.58216 / 0.30 (33885) SS BOND : bond 0.00570 / 0.39 ( 42) SS BOND : angle 2.30893 / 1.75 ( 84) hydrogen bonds : bond 0.03697 / 2.44 ( 850) hydrogen bonds : angle 4.77213 / 3.24 ( 2583) link_ALPHA1-3 : bond 0.00723 / 0.37 ( 3) link_ALPHA1-3 : angle 1.65509 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00975 / 0.49 ( 3) link_ALPHA1-6 : angle 1.59203 / 1.10 ( 9) link_BETA1-4 : bond 0.00358 / 0.24 ( 12) link_BETA1-4 : angle 1.49119 / 1.08 ( 36) link_NAG-ASN : bond 0.00159 / 0.10 ( 36) link_NAG-ASN : angle 2.19268 / 1.51 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 565 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6549 (m-80) cc_final: 0.6066 (t80) REVERT: A 176 PHE cc_start: 0.7918 (m-80) cc_final: 0.7415 (m-80) REVERT: A 213 TYR cc_start: 0.6944 (m-80) cc_final: 0.6254 (m-80) REVERT: A 227 TYR cc_start: 0.7181 (p90) cc_final: 0.6789 (p90) REVERT: A 276 ASN cc_start: 0.7362 (t0) cc_final: 0.6848 (p0) REVERT: A 396 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7647 (mtt180) REVERT: A 509 ASP cc_start: 0.7344 (p0) cc_final: 0.6807 (p0) REVERT: A 556 ASN cc_start: 0.5243 (t0) cc_final: 0.4973 (t0) REVERT: A 578 SER cc_start: 0.8437 (m) cc_final: 0.8151 (t) REVERT: A 614 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7462 (ptmm) REVERT: A 615 PHE cc_start: 0.7888 (m-80) cc_final: 0.7608 (m-80) REVERT: A 624 LYS cc_start: 0.7526 (tppp) cc_final: 0.7217 (tppp) REVERT: A 644 MET cc_start: 0.7607 (ptm) cc_final: 0.7356 (ptp) REVERT: A 651 LYS cc_start: 0.8355 (tttt) cc_final: 0.7743 (ttpt) REVERT: A 669 SER cc_start: 0.8279 (t) cc_final: 0.7851 (p) REVERT: A 674 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8470 (t) REVERT: A 680 SER cc_start: 0.8771 (p) cc_final: 0.8288 (m) REVERT: A 687 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8226 (tttp) REVERT: A 704 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6588 (mp0) REVERT: A 728 THR cc_start: 0.8131 (t) cc_final: 0.7913 (p) REVERT: A 730 GLU cc_start: 0.7445 (tt0) cc_final: 0.7207 (tt0) REVERT: A 814 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8333 (t0) REVERT: A 821 GLN cc_start: 0.8023 (tt0) cc_final: 0.7173 (tm-30) REVERT: A 856 GLU cc_start: 0.7139 (pm20) cc_final: 0.6550 (pm20) REVERT: A 857 GLU cc_start: 0.7675 (mp0) cc_final: 0.6594 (mp0) REVERT: A 870 ASP cc_start: 0.6394 (t70) cc_final: 0.6104 (t0) REVERT: A 924 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.7138 (mmt180) REVERT: A 941 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 948 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6838 (tm-30) REVERT: A 951 HIS cc_start: 0.7874 (t70) cc_final: 0.7461 (t-90) REVERT: A 954 SER cc_start: 0.8622 (m) cc_final: 0.8236 (p) REVERT: A 1005 SER cc_start: 0.8811 (m) cc_final: 0.8392 (p) REVERT: A 1104 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7631 (mmtp) REVERT: A 1109 GLN cc_start: 0.7519 (tp40) cc_final: 0.7102 (tp40) REVERT: A 1211 GLU cc_start: 0.7067 (mp0) cc_final: 0.6797 (mp0) REVERT: A 1230 TYR cc_start: 0.7493 (m-10) cc_final: 0.7034 (m-80) REVERT: B 212 TYR cc_start: 0.8204 (m-80) cc_final: 0.7952 (m-10) REVERT: B 214 MET cc_start: 0.7121 (tpt) cc_final: 0.6848 (tpt) REVERT: B 225 ILE cc_start: 0.8421 (mt) cc_final: 0.8125 (tp) REVERT: B 257 ASN cc_start: 0.7854 (t0) cc_final: 0.7405 (t0) REVERT: B 351 ASN cc_start: 0.7157 (p0) cc_final: 0.6852 (p0) REVERT: B 372 TYR cc_start: 0.6282 (m-10) cc_final: 0.5789 (m-10) REVERT: B 438 PHE cc_start: 0.8593 (m-80) cc_final: 0.8307 (m-10) REVERT: B 444 THR cc_start: 0.8122 (p) cc_final: 0.7811 (p) REVERT: B 507 PHE cc_start: 0.7805 (p90) cc_final: 0.7545 (p90) REVERT: B 509 ASP cc_start: 0.7737 (t0) cc_final: 0.6817 (p0) REVERT: B 593 SER cc_start: 0.8128 (m) cc_final: 0.7657 (p) REVERT: B 651 LYS cc_start: 0.8219 (tttt) cc_final: 0.7570 (mmmm) REVERT: B 660 GLU cc_start: 0.6747 (mp0) cc_final: 0.6398 (mp0) REVERT: B 668 SER cc_start: 0.8891 (t) cc_final: 0.8493 (p) REVERT: B 670 PHE cc_start: 0.8363 (m-10) cc_final: 0.7629 (m-80) REVERT: B 679 ASP cc_start: 0.7730 (m-30) cc_final: 0.7500 (m-30) REVERT: B 740 ASP cc_start: 0.6904 (t0) cc_final: 0.6453 (t0) REVERT: B 757 CYS cc_start: 0.5944 (t) cc_final: 0.5500 (t) REVERT: B 758 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8359 (ttmm) REVERT: B 768 GLN cc_start: 0.7649 (mt0) cc_final: 0.7327 (mt0) REVERT: B 771 GLN cc_start: 0.7921 (pm20) cc_final: 0.7625 (pm20) REVERT: B 773 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7983 (ttmt) REVERT: B 795 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: B 844 GLU cc_start: 0.7529 (tp30) cc_final: 0.7058 (tp30) REVERT: B 847 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7241 (mt-10) REVERT: B 945 VAL cc_start: 0.8445 (p) cc_final: 0.8175 (m) REVERT: B 954 SER cc_start: 0.8291 (m) cc_final: 0.7878 (p) REVERT: B 979 GLN cc_start: 0.7279 (tp40) cc_final: 0.6668 (tm-30) REVERT: B 1039 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7025 (mp10) REVERT: B 1069 ASP cc_start: 0.7071 (t0) cc_final: 0.6792 (t0) REVERT: B 1084 ASP cc_start: 0.7188 (t70) cc_final: 0.6882 (t0) REVERT: B 1107 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7266 (mt-10) REVERT: B 1117 GLN cc_start: 0.7600 (mt0) cc_final: 0.7363 (tt0) REVERT: B 1138 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 1184 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 35 PHE cc_start: 0.8458 (t80) cc_final: 0.7952 (t80) REVERT: C 152 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8351 (ptmm) REVERT: C 176 PHE cc_start: 0.7828 (m-80) cc_final: 0.7504 (m-10) REVERT: C 179 LYS cc_start: 0.7705 (pttp) cc_final: 0.7448 (pttm) REVERT: C 185 PHE cc_start: 0.8062 (t80) cc_final: 0.7654 (t80) REVERT: C 204 MET cc_start: 0.6452 (mtt) cc_final: 0.6235 (mtt) REVERT: C 211 THR cc_start: 0.7895 (m) cc_final: 0.7574 (p) REVERT: C 213 TYR cc_start: 0.8021 (m-80) cc_final: 0.7468 (m-80) REVERT: C 247 ASN cc_start: 0.7838 (p0) cc_final: 0.7332 (p0) REVERT: C 291 TYR cc_start: 0.7413 (m-10) cc_final: 0.7155 (m-10) REVERT: C 299 PHE cc_start: 0.8566 (m-80) cc_final: 0.8023 (m-80) REVERT: C 317 GLU cc_start: 0.7138 (tp30) cc_final: 0.6569 (tp30) REVERT: C 354 ASP cc_start: 0.7133 (t0) cc_final: 0.6481 (t0) REVERT: C 418 LEU cc_start: 0.8190 (mt) cc_final: 0.7918 (mp) REVERT: C 456 THR cc_start: 0.7900 (m) cc_final: 0.7680 (m) REVERT: C 463 TYR cc_start: 0.8237 (m-80) cc_final: 0.7894 (m-80) REVERT: C 512 PHE cc_start: 0.6716 (m-80) cc_final: 0.6305 (m-80) REVERT: C 555 TYR cc_start: 0.6746 (m-80) cc_final: 0.6259 (m-80) REVERT: C 566 ASN cc_start: 0.7755 (t0) cc_final: 0.7317 (t0) REVERT: C 569 ASP cc_start: 0.7493 (t70) cc_final: 0.7112 (t0) REVERT: C 581 ASP cc_start: 0.7427 (t0) cc_final: 0.6924 (t0) REVERT: C 590 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (m) REVERT: C 615 PHE cc_start: 0.8048 (m-80) cc_final: 0.7840 (m-80) REVERT: C 616 THR cc_start: 0.8375 (t) cc_final: 0.8070 (m) REVERT: C 624 LYS cc_start: 0.7903 (tppt) cc_final: 0.7567 (tppt) REVERT: C 640 ASP cc_start: 0.6926 (t0) cc_final: 0.6613 (t70) REVERT: C 651 LYS cc_start: 0.8326 (ttpt) cc_final: 0.7924 (ttmm) REVERT: C 745 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7743 (p) REVERT: C 825 GLN cc_start: 0.8090 (pp30) cc_final: 0.7737 (pp30) REVERT: C 843 LEU cc_start: 0.8033 (tp) cc_final: 0.7819 (tt) REVERT: C 857 GLU cc_start: 0.7250 (tp30) cc_final: 0.6877 (tp30) REVERT: C 874 PHE cc_start: 0.8121 (m-80) cc_final: 0.7555 (m-80) REVERT: C 876 ASN cc_start: 0.8124 (m-40) cc_final: 0.7915 (m-40) REVERT: C 957 LEU cc_start: 0.8210 (mt) cc_final: 0.7891 (mp) REVERT: C 979 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7569 (tp40) REVERT: C 1069 ASP cc_start: 0.6677 (t0) cc_final: 0.6470 (t0) REVERT: C 1107 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: C 1120 ASN cc_start: 0.7845 (m-40) cc_final: 0.7431 (m-40) REVERT: C 1127 SER cc_start: 0.7919 (t) cc_final: 0.7623 (p) REVERT: C 1156 THR cc_start: 0.8110 (m) cc_final: 0.7694 (p) REVERT: C 1220 PHE cc_start: 0.8001 (m-80) cc_final: 0.7548 (m-80) outliers start: 93 outliers final: 78 residues processed: 606 average time/residue: 0.1691 time to fit residues: 161.9740 Evaluate side-chains 645 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 559 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1191 THR Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1158 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 954 SER Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 78 optimal weight: 0.0050 chunk 132 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 273 optimal weight: 0.0170 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 overall best weight: 0.4832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 621 GLN A1139 HIS B 528 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN C 40 ASN C 996 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105558 restraints weight = 39124.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108988 restraints weight = 18746.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111171 restraints weight = 10864.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112613 restraints weight = 7293.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113384 restraints weight = 5445.623| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25014 Z= 0.119 Angle : 0.605 14.442 34131 Z= 0.306 Chirality : 0.044 0.333 4117 Planarity : 0.004 0.049 4250 Dihedral : 6.774 102.154 4385 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.40 % Allowed : 17.17 % Favored : 79.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2990 helix: 1.97 (0.21), residues: 624 sheet: -0.31 (0.20), residues: 741 loop : -0.99 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1235 TYR 0.023 0.001 TYR C 934 PHE 0.035 0.001 PHE A 387 TRP 0.013 0.001 TRP C 168 HIS 0.013 0.001 HIS B1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (24918) covalent geometry : angle 0.58476 / 0.30 (33885) SS BOND : bond 0.00542 / 0.37 ( 42) SS BOND : angle 2.33110 / 1.75 ( 84) hydrogen bonds : bond 0.03520 / 2.32 ( 850) hydrogen bonds : angle 4.68427 / 3.18 ( 2583) link_ALPHA1-3 : bond 0.00843 / 0.43 ( 3) link_ALPHA1-3 : angle 1.63000 / 1.18 ( 9) link_ALPHA1-6 : bond 0.01011 / 0.51 ( 3) link_ALPHA1-6 : angle 1.63857 / 1.12 ( 9) link_BETA1-4 : bond 0.00381 / 0.26 ( 12) link_BETA1-4 : angle 1.44682 / 1.05 ( 36) link_NAG-ASN : bond 0.00247 / 0.17 ( 36) link_NAG-ASN : angle 1.77569 / 1.24 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 570 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6561 (m-80) cc_final: 0.6138 (t80) REVERT: A 176 PHE cc_start: 0.7937 (m-80) cc_final: 0.7430 (m-80) REVERT: A 213 TYR cc_start: 0.6953 (m-80) cc_final: 0.6270 (m-80) REVERT: A 227 TYR cc_start: 0.7173 (p90) cc_final: 0.6786 (p90) REVERT: A 276 ASN cc_start: 0.7383 (t0) cc_final: 0.6850 (p0) REVERT: A 396 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7578 (mtt180) REVERT: A 411 PHE cc_start: 0.7422 (t80) cc_final: 0.7056 (t80) REVERT: A 481 ASP cc_start: 0.7148 (t0) cc_final: 0.6936 (t0) REVERT: A 482 ASP cc_start: 0.6726 (p0) cc_final: 0.6508 (p0) REVERT: A 509 ASP cc_start: 0.7335 (p0) cc_final: 0.7025 (p0) REVERT: A 556 ASN cc_start: 0.5264 (t0) cc_final: 0.4987 (t0) REVERT: A 578 SER cc_start: 0.8402 (m) cc_final: 0.7898 (p) REVERT: A 615 PHE cc_start: 0.7882 (m-80) cc_final: 0.7673 (m-80) REVERT: A 624 LYS cc_start: 0.7529 (tppp) cc_final: 0.7231 (tppp) REVERT: A 644 MET cc_start: 0.7585 (ptm) cc_final: 0.7341 (ptp) REVERT: A 651 LYS cc_start: 0.8339 (tttt) cc_final: 0.7749 (ttpt) REVERT: A 669 SER cc_start: 0.8281 (t) cc_final: 0.7860 (p) REVERT: A 674 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8452 (t) REVERT: A 680 SER cc_start: 0.8746 (p) cc_final: 0.8257 (m) REVERT: A 687 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8226 (tttp) REVERT: A 704 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6549 (mp0) REVERT: A 728 THR cc_start: 0.8128 (t) cc_final: 0.7907 (p) REVERT: A 730 GLU cc_start: 0.7471 (tt0) cc_final: 0.7195 (tt0) REVERT: A 814 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8325 (t0) REVERT: A 821 GLN cc_start: 0.8008 (tt0) cc_final: 0.7141 (tm-30) REVERT: A 856 GLU cc_start: 0.7120 (pm20) cc_final: 0.6552 (pm20) REVERT: A 857 GLU cc_start: 0.7651 (mp0) cc_final: 0.6611 (mp0) REVERT: A 870 ASP cc_start: 0.6417 (t70) cc_final: 0.6105 (t0) REVERT: A 924 ARG cc_start: 0.7428 (mmp-170) cc_final: 0.7155 (mmt180) REVERT: A 941 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 948 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6901 (tm-30) REVERT: A 954 SER cc_start: 0.8612 (m) cc_final: 0.8231 (p) REVERT: A 1005 SER cc_start: 0.8794 (m) cc_final: 0.8363 (p) REVERT: A 1104 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7617 (mmtp) REVERT: A 1109 GLN cc_start: 0.7472 (tp40) cc_final: 0.7008 (tp40) REVERT: A 1230 TYR cc_start: 0.7465 (m-10) cc_final: 0.6928 (m-80) REVERT: B 212 TYR cc_start: 0.8217 (m-80) cc_final: 0.7979 (m-10) REVERT: B 213 TYR cc_start: 0.7199 (m-80) cc_final: 0.6866 (m-80) REVERT: B 225 ILE cc_start: 0.8420 (mt) cc_final: 0.8064 (tp) REVERT: B 257 ASN cc_start: 0.7839 (t0) cc_final: 0.7387 (t0) REVERT: B 351 ASN cc_start: 0.7169 (p0) cc_final: 0.6850 (p0) REVERT: B 372 TYR cc_start: 0.6191 (m-10) cc_final: 0.5699 (m-10) REVERT: B 438 PHE cc_start: 0.8551 (m-80) cc_final: 0.8269 (m-80) REVERT: B 444 THR cc_start: 0.8109 (p) cc_final: 0.7782 (p) REVERT: B 509 ASP cc_start: 0.7751 (t0) cc_final: 0.6887 (p0) REVERT: B 593 SER cc_start: 0.8139 (m) cc_final: 0.7667 (p) REVERT: B 651 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7609 (mmmm) REVERT: B 660 GLU cc_start: 0.6702 (mp0) cc_final: 0.6376 (mp0) REVERT: B 668 SER cc_start: 0.8835 (t) cc_final: 0.8596 (p) REVERT: B 679 ASP cc_start: 0.7708 (m-30) cc_final: 0.7477 (m-30) REVERT: B 740 ASP cc_start: 0.6890 (t0) cc_final: 0.6436 (t0) REVERT: B 757 CYS cc_start: 0.5914 (t) cc_final: 0.5478 (t) REVERT: B 758 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8373 (ttmm) REVERT: B 768 GLN cc_start: 0.7622 (mt0) cc_final: 0.7338 (mt0) REVERT: B 771 GLN cc_start: 0.7910 (pm20) cc_final: 0.7627 (pm20) REVERT: B 773 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7999 (ttmt) REVERT: B 795 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: B 844 GLU cc_start: 0.7464 (tp30) cc_final: 0.6958 (tp30) REVERT: B 847 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 945 VAL cc_start: 0.8410 (p) cc_final: 0.8138 (m) REVERT: B 954 SER cc_start: 0.8261 (m) cc_final: 0.7856 (p) REVERT: B 979 GLN cc_start: 0.7244 (tp40) cc_final: 0.6713 (tm-30) REVERT: B 1084 ASP cc_start: 0.7091 (t70) cc_final: 0.6780 (t0) REVERT: B 1107 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7245 (mt-10) REVERT: B 1117 GLN cc_start: 0.7550 (mt0) cc_final: 0.7346 (tt0) REVERT: B 1167 ILE cc_start: 0.8678 (mm) cc_final: 0.8373 (mm) REVERT: B 1184 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 1207 ARG cc_start: 0.7906 (mmm-85) cc_final: 0.7611 (mmm-85) REVERT: C 35 PHE cc_start: 0.8476 (t80) cc_final: 0.7961 (t80) REVERT: C 152 LYS cc_start: 0.8872 (ptmt) cc_final: 0.8328 (ptmm) REVERT: C 176 PHE cc_start: 0.7806 (m-80) cc_final: 0.7482 (m-10) REVERT: C 179 LYS cc_start: 0.7700 (pttp) cc_final: 0.7439 (pttm) REVERT: C 185 PHE cc_start: 0.8045 (t80) cc_final: 0.7618 (t80) REVERT: C 211 THR cc_start: 0.7892 (m) cc_final: 0.7587 (p) REVERT: C 213 TYR cc_start: 0.7990 (m-80) cc_final: 0.7435 (m-80) REVERT: C 247 ASN cc_start: 0.7856 (p0) cc_final: 0.7331 (p0) REVERT: C 291 TYR cc_start: 0.7441 (m-10) cc_final: 0.7152 (m-10) REVERT: C 299 PHE cc_start: 0.8554 (m-80) cc_final: 0.8016 (m-80) REVERT: C 317 GLU cc_start: 0.7113 (tp30) cc_final: 0.6667 (tp30) REVERT: C 354 ASP cc_start: 0.7165 (t0) cc_final: 0.6522 (t0) REVERT: C 418 LEU cc_start: 0.8200 (mt) cc_final: 0.7923 (mp) REVERT: C 463 TYR cc_start: 0.8231 (m-80) cc_final: 0.7886 (m-80) REVERT: C 512 PHE cc_start: 0.6698 (m-80) cc_final: 0.6285 (m-80) REVERT: C 555 TYR cc_start: 0.6794 (m-80) cc_final: 0.6358 (m-80) REVERT: C 566 ASN cc_start: 0.7722 (t0) cc_final: 0.7296 (t0) REVERT: C 569 ASP cc_start: 0.7472 (t70) cc_final: 0.7085 (t0) REVERT: C 581 ASP cc_start: 0.7401 (t0) cc_final: 0.6904 (t0) REVERT: C 590 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8308 (m) REVERT: C 616 THR cc_start: 0.8318 (t) cc_final: 0.8023 (m) REVERT: C 624 LYS cc_start: 0.7866 (tppt) cc_final: 0.7546 (tppt) REVERT: C 640 ASP cc_start: 0.6932 (t0) cc_final: 0.6614 (t70) REVERT: C 651 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7914 (ttmm) REVERT: C 732 PRO cc_start: 0.8708 (Cg_exo) cc_final: 0.8508 (Cg_endo) REVERT: C 745 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7689 (p) REVERT: C 825 GLN cc_start: 0.8078 (pp30) cc_final: 0.7727 (pp30) REVERT: C 843 LEU cc_start: 0.8001 (tp) cc_final: 0.7790 (tt) REVERT: C 857 GLU cc_start: 0.7224 (tp30) cc_final: 0.6711 (tp30) REVERT: C 874 PHE cc_start: 0.8119 (m-80) cc_final: 0.7543 (m-80) REVERT: C 876 ASN cc_start: 0.8112 (m-40) cc_final: 0.7886 (m-40) REVERT: C 957 LEU cc_start: 0.8203 (mt) cc_final: 0.7975 (mp) REVERT: C 979 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7500 (tp40) REVERT: C 1107 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6723 (tm-30) REVERT: C 1120 ASN cc_start: 0.7846 (m-40) cc_final: 0.7438 (m-40) REVERT: C 1127 SER cc_start: 0.7896 (t) cc_final: 0.7595 (p) REVERT: C 1220 PHE cc_start: 0.7999 (m-80) cc_final: 0.7521 (m-80) outliers start: 91 outliers final: 71 residues processed: 611 average time/residue: 0.1670 time to fit residues: 161.3693 Evaluate side-chains 636 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 557 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 651 LYS Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 954 SER Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 268 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 158 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 301 GLN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN B 979 GLN C 40 ASN C 801 ASN C 988 GLN C1126 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096622 restraints weight = 41111.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099768 restraints weight = 20716.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101761 restraints weight = 12463.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103137 restraints weight = 8646.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103989 restraints weight = 6589.810| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 25014 Z= 0.140 Angle : 0.619 14.722 34131 Z= 0.315 Chirality : 0.044 0.358 4117 Planarity : 0.004 0.053 4250 Dihedral : 6.787 99.985 4385 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.33 % Allowed : 17.47 % Favored : 79.20 % 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: -0.28 (0.15), residues: 2990 helix: 1.95 (0.21), residues: 624 sheet: -0.27 (0.20), residues: 721 loop : -1.00 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 314 TYR 0.024 0.001 TYR C 934 PHE 0.037 0.001 PHE A 387 TRP 0.011 0.001 TRP C 168 HIS 0.014 0.001 HIS B1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (24918) covalent geometry : angle 0.59827 / 0.31 (33885) SS BOND : bond 0.00543 / 0.38 ( 42) SS BOND : angle 2.36770 / 1.72 ( 84) hydrogen bonds : bond 0.03707 / 2.45 ( 850) hydrogen bonds : angle 4.69596 / 3.19 ( 2583) link_ALPHA1-3 : bond 0.00737 / 0.37 ( 3) link_ALPHA1-3 : angle 1.66839 / 1.20 ( 9) link_ALPHA1-6 : bond 0.00952 / 0.48 ( 3) link_ALPHA1-6 : angle 1.68306 / 1.13 ( 9) link_BETA1-4 : bond 0.00355 / 0.23 ( 12) link_BETA1-4 : angle 1.48922 / 1.07 ( 36) link_NAG-ASN : bond 0.00349 / 0.24 ( 36) link_NAG-ASN : angle 1.83018 / 1.27 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5980 Ramachandran restraints generated. 2990 Oldfield, 0 Emsley, 2990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 567 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.6508 (m-80) cc_final: 0.6117 (t80) REVERT: A 176 PHE cc_start: 0.7923 (m-80) cc_final: 0.7449 (m-80) REVERT: A 213 TYR cc_start: 0.6931 (m-80) cc_final: 0.6320 (m-80) REVERT: A 227 TYR cc_start: 0.7126 (p90) cc_final: 0.6733 (p90) REVERT: A 276 ASN cc_start: 0.7451 (t0) cc_final: 0.6843 (p0) REVERT: A 396 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7664 (mtt180) REVERT: A 482 ASP cc_start: 0.6798 (p0) cc_final: 0.6582 (p0) REVERT: A 509 ASP cc_start: 0.7352 (p0) cc_final: 0.7009 (p0) REVERT: A 556 ASN cc_start: 0.5476 (t0) cc_final: 0.5198 (t0) REVERT: A 578 SER cc_start: 0.8446 (m) cc_final: 0.7985 (p) REVERT: A 588 PHE cc_start: 0.7648 (t80) cc_final: 0.7058 (t80) REVERT: A 624 LYS cc_start: 0.7502 (tppp) cc_final: 0.7230 (tppp) REVERT: A 644 MET cc_start: 0.7534 (ptm) cc_final: 0.7310 (ptp) REVERT: A 651 LYS cc_start: 0.8357 (tttt) cc_final: 0.7828 (ttpt) REVERT: A 669 SER cc_start: 0.8217 (t) cc_final: 0.7826 (p) REVERT: A 674 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8448 (t) REVERT: A 680 SER cc_start: 0.8737 (p) cc_final: 0.8292 (m) REVERT: A 687 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8267 (tttp) REVERT: A 728 THR cc_start: 0.8119 (t) cc_final: 0.7870 (p) REVERT: A 730 GLU cc_start: 0.7330 (tt0) cc_final: 0.7077 (tt0) REVERT: A 814 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8333 (t0) REVERT: A 821 GLN cc_start: 0.7934 (tt0) cc_final: 0.7181 (tm-30) REVERT: A 856 GLU cc_start: 0.7040 (pm20) cc_final: 0.6514 (pm20) REVERT: A 857 GLU cc_start: 0.7588 (mp0) cc_final: 0.6581 (mp0) REVERT: A 870 ASP cc_start: 0.6365 (t70) cc_final: 0.6092 (t0) REVERT: A 924 ARG cc_start: 0.7366 (mmp-170) cc_final: 0.7083 (mmt180) REVERT: A 941 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 948 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 954 SER cc_start: 0.8752 (m) cc_final: 0.8355 (p) REVERT: A 1005 SER cc_start: 0.8848 (m) cc_final: 0.8442 (p) REVERT: A 1104 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7734 (mmtp) REVERT: A 1109 GLN cc_start: 0.7445 (tp40) cc_final: 0.7034 (tp40) REVERT: A 1230 TYR cc_start: 0.7427 (m-10) cc_final: 0.7058 (m-80) REVERT: B 225 ILE cc_start: 0.8415 (mt) cc_final: 0.8092 (tp) REVERT: B 227 TYR cc_start: 0.7503 (p90) cc_final: 0.6970 (p90) REVERT: B 257 ASN cc_start: 0.7812 (t0) cc_final: 0.7407 (t0) REVERT: B 351 ASN cc_start: 0.7159 (p0) cc_final: 0.6832 (p0) REVERT: B 372 TYR cc_start: 0.6261 (m-10) cc_final: 0.5765 (m-10) REVERT: B 438 PHE cc_start: 0.8510 (m-80) cc_final: 0.8219 (m-80) REVERT: B 444 THR cc_start: 0.8184 (p) cc_final: 0.7867 (p) REVERT: B 509 ASP cc_start: 0.7765 (t0) cc_final: 0.7011 (p0) REVERT: B 593 SER cc_start: 0.8175 (m) cc_final: 0.7760 (p) REVERT: B 651 LYS cc_start: 0.8308 (tttt) cc_final: 0.7533 (mmmm) REVERT: B 660 GLU cc_start: 0.6677 (mp0) cc_final: 0.6431 (mp0) REVERT: B 668 SER cc_start: 0.8874 (t) cc_final: 0.8501 (p) REVERT: B 670 PHE cc_start: 0.8377 (m-10) cc_final: 0.7668 (m-80) REVERT: B 679 ASP cc_start: 0.7599 (m-30) cc_final: 0.7370 (m-30) REVERT: B 740 ASP cc_start: 0.6834 (t0) cc_final: 0.6472 (t0) REVERT: B 757 CYS cc_start: 0.5840 (t) cc_final: 0.5405 (t) REVERT: B 758 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8363 (ttmm) REVERT: B 768 GLN cc_start: 0.7588 (mt0) cc_final: 0.7305 (mt0) REVERT: B 771 GLN cc_start: 0.7856 (pm20) cc_final: 0.7596 (pm20) REVERT: B 773 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7942 (ttmt) REVERT: B 795 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: B 844 GLU cc_start: 0.7455 (tp30) cc_final: 0.7007 (tp30) REVERT: B 847 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7169 (mt-10) REVERT: B 945 VAL cc_start: 0.8391 (p) cc_final: 0.8123 (m) REVERT: B 954 SER cc_start: 0.8298 (m) cc_final: 0.7884 (p) REVERT: B 979 GLN cc_start: 0.7170 (tp-100) cc_final: 0.6681 (tm-30) REVERT: B 1039 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: B 1084 ASP cc_start: 0.7026 (t70) cc_final: 0.6726 (t0) REVERT: B 1107 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7171 (mt-10) REVERT: B 1117 GLN cc_start: 0.7628 (mt0) cc_final: 0.7390 (tt0) REVERT: B 1167 ILE cc_start: 0.8706 (mm) cc_final: 0.8417 (mm) REVERT: B 1184 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7017 (mm-30) REVERT: C 35 PHE cc_start: 0.8445 (t80) cc_final: 0.7929 (t80) REVERT: C 152 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8335 (ptmm) REVERT: C 176 PHE cc_start: 0.7818 (m-80) cc_final: 0.7527 (m-10) REVERT: C 179 LYS cc_start: 0.7751 (pttp) cc_final: 0.7482 (pttm) REVERT: C 185 PHE cc_start: 0.8031 (t80) cc_final: 0.7664 (t80) REVERT: C 204 MET cc_start: 0.6114 (mtt) cc_final: 0.5721 (mtt) REVERT: C 211 THR cc_start: 0.7934 (m) cc_final: 0.7665 (p) REVERT: C 213 TYR cc_start: 0.8026 (m-80) cc_final: 0.7458 (m-80) REVERT: C 247 ASN cc_start: 0.7914 (p0) cc_final: 0.7390 (p0) REVERT: C 291 TYR cc_start: 0.7467 (m-10) cc_final: 0.7210 (m-10) REVERT: C 299 PHE cc_start: 0.8559 (m-80) cc_final: 0.8030 (m-80) REVERT: C 317 GLU cc_start: 0.7060 (tp30) cc_final: 0.6786 (tp30) REVERT: C 354 ASP cc_start: 0.7136 (t0) cc_final: 0.6548 (t0) REVERT: C 418 LEU cc_start: 0.8275 (mt) cc_final: 0.8057 (mp) REVERT: C 463 TYR cc_start: 0.8292 (m-80) cc_final: 0.7976 (m-80) REVERT: C 512 PHE cc_start: 0.6755 (m-80) cc_final: 0.6338 (m-80) REVERT: C 555 TYR cc_start: 0.6733 (m-80) cc_final: 0.6307 (m-80) REVERT: C 566 ASN cc_start: 0.7657 (t0) cc_final: 0.7239 (t0) REVERT: C 569 ASP cc_start: 0.7501 (t70) cc_final: 0.7145 (t0) REVERT: C 581 ASP cc_start: 0.7341 (t0) cc_final: 0.6901 (t0) REVERT: C 590 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8349 (m) REVERT: C 624 LYS cc_start: 0.7861 (tppt) cc_final: 0.7519 (tppt) REVERT: C 640 ASP cc_start: 0.6886 (t0) cc_final: 0.6605 (t70) REVERT: C 651 LYS cc_start: 0.8267 (ttpt) cc_final: 0.8014 (ttmm) REVERT: C 745 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7673 (p) REVERT: C 825 GLN cc_start: 0.8066 (pp30) cc_final: 0.7741 (pp30) REVERT: C 834 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: C 843 LEU cc_start: 0.8172 (tp) cc_final: 0.7947 (tt) REVERT: C 857 GLU cc_start: 0.7198 (tp30) cc_final: 0.6715 (tp30) REVERT: C 874 PHE cc_start: 0.8102 (m-80) cc_final: 0.7538 (m-80) REVERT: C 876 ASN cc_start: 0.8075 (m-40) cc_final: 0.7860 (m-40) REVERT: C 957 LEU cc_start: 0.8238 (mt) cc_final: 0.7936 (mp) REVERT: C 979 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7537 (tp40) REVERT: C 1107 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: C 1120 ASN cc_start: 0.7910 (m-40) cc_final: 0.7501 (m-40) REVERT: C 1127 SER cc_start: 0.7942 (t) cc_final: 0.7597 (p) REVERT: C 1209 MET cc_start: 0.6482 (tpp) cc_final: 0.6281 (tpp) REVERT: C 1220 PHE cc_start: 0.7985 (m-80) cc_final: 0.7543 (m-80) outliers start: 89 outliers final: 76 residues processed: 610 average time/residue: 0.1667 time to fit residues: 161.4273 Evaluate side-chains 646 residues out of total 2673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 561 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 814 ASN Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1078 SER Chi-restraints excluded: chain A residue 1122 CYS Chi-restraints excluded: chain A residue 1227 VAL Chi-restraints excluded: chain A residue 1228 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 272 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 978 VAL Chi-restraints excluded: chain B residue 1039 GLN Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1191 THR Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 568 GLN Chi-restraints excluded: chain C residue 572 CYS Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 678 SER Chi-restraints excluded: chain C residue 745 THR Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 929 LEU Chi-restraints excluded: chain C residue 954 SER Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1037 LYS Chi-restraints excluded: chain C residue 1045 GLN Chi-restraints excluded: chain C residue 1107 GLU Chi-restraints excluded: chain C residue 1221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 61 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 303 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN ** A1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 801 ASN C1126 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1222 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 = 0.3486 r_free = 0.3486 target = 0.118956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100765 restraints weight = 40088.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104215 restraints weight = 19221.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106474 restraints weight = 11146.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107892 restraints weight = 7418.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108895 restraints weight = 5552.598| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 25014 Z= 0.202 Angle : 0.667 14.630 34131 Z= 0.339 Chirality : 0.045 0.354 4117 Planarity : 0.004 0.057 4250 Dihedral : 7.039 102.016 4385 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.29 % Allowed : 17.99 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2990 helix: 1.77 (0.20), residues: 625 sheet: -0.28 (0.20), residues: 718 loop : -1.06 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 314 TYR 0.027 0.002 TYR C 934 PHE 0.020 0.002 PHE A 615 TRP 0.010 0.001 TRP C 168 HIS 0.014 0.001 HIS B1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (24918) covalent geometry : angle 0.64422 / 0.33 (33885) SS BOND : bond 0.00572 / 0.39 ( 42) SS BOND : angle 2.57554 / 1.83 ( 84) hydrogen bonds : bond 0.04100 / 2.71 ( 850) hydrogen bonds : angle 4.82298 / 3.27 ( 2583) link_ALPHA1-3 : bond 0.00652 / 0.33 ( 3) link_ALPHA1-3 : angle 1.79267 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00959 / 0.48 ( 3) link_ALPHA1-6 : angle 1.73958 / 1.15 ( 9) link_BETA1-4 : bond 0.00333 / 0.21 ( 12) link_BETA1-4 : angle 1.62932 / 1.17 ( 36) link_NAG-ASN : bond 0.00362 / 0.24 ( 36) link_NAG-ASN : angle 1.97912 / 1.36 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4525.94 seconds wall clock time: 78 minutes 55.62 seconds (4735.62 seconds total)