Starting phenix.real_space_refine on Tue Aug 26 10:05:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynz_33976/08_2025/7ynz_33976.cif" } resolution = 3.5 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Mg 4 5.21 5 S 228 5.16 5 C 23160 2.51 5 N 6040 2.21 5 O 6404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35844 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 7034 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 27, 'TRANS': 854} Chain breaks: 5 Chain: "B" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1924 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 239} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 7034 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 27, 'TRANS': 854} Chain breaks: 5 Chain: "D" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1924 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 239} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 7034 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 27, 'TRANS': 854} Chain breaks: 5 Chain: "F" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1924 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 239} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 7034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 882, 7034 Classifications: {'peptide': 882} Link IDs: {'PTRANS': 27, 'TRANS': 854} Chain breaks: 5 Chain: "H" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1924 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 239} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 3, ' MG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.71, per 1000 atoms: 0.24 Number of scatterers: 35844 At special positions: 0 Unit cell: (163.344, 160.356, 176.292, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 228 16.00 Mg 4 11.99 O 6404 8.00 N 6040 7.00 C 23160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 57 " distance=2.02 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 57 " distance=2.02 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 207 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 49 " distance=2.03 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 57 " distance=2.03 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 47 " - pdb=" SG CYS H 57 " distance=2.03 Simple disulfide: pdb=" SG CYS H 205 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 207 " - pdb=" SG CYS H 253 " 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 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8600 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 28 sheets defined 49.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 21 through 49 removed outlier: 3.999A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 171 Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.537A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.755A pdb=" N VAL A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.427A pdb=" N PHE A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 259 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 removed outlier: 4.071A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.763A pdb=" N LYS A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.537A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.771A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.801A pdb=" N VAL A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.707A pdb=" N LEU A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.519A pdb=" N VAL A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.005A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.958A pdb=" N LEU A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 916 through 921 removed outlier: 3.841A pdb=" N ASP A 921 " --> pdb=" O SER A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.659A pdb=" N PHE A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.209A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 956 removed outlier: 4.079A pdb=" N LEU A 949 " --> pdb=" O ALA A 945 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 950 " --> pdb=" O THR A 946 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 951 " --> pdb=" O PRO A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 971 Processing helix chain 'A' and resid 985 through 989 removed outlier: 4.095A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.882A pdb=" N LEU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 164' Processing helix chain 'B' and resid 186 through 190 removed outlier: 3.684A pdb=" N ARG B 189 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.825A pdb=" N TRP B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.707A pdb=" N PHE B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 259 through 297 removed outlier: 3.585A pdb=" N ALA B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 3.507A pdb=" N LEU B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 148 through 171 Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.575A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.629A pdb=" N VAL C 193 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.544A pdb=" N PHE C 208 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 229 through 259 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 removed outlier: 3.796A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET C 314 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 393 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.551A pdb=" N SER C 418 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.722A pdb=" N LYS C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.857A pdb=" N PHE C 511 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.823A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 555 removed outlier: 3.645A pdb=" N VAL C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 759 through 766 removed outlier: 3.797A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 806 through 809 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.029A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 890 removed outlier: 3.713A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 916 through 920 removed outlier: 3.508A pdb=" N VAL C 919 " --> pdb=" O ALA C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.441A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 929 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 939 removed outlier: 4.286A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 970 through 974 removed outlier: 3.617A pdb=" N ASP C 973 " --> pdb=" O ALA C 970 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C 974 " --> pdb=" O ASN C 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 970 through 974' Processing helix chain 'C' and resid 987 through 994 removed outlier: 4.012A pdb=" N GLY C 994 " --> pdb=" O LEU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.586A pdb=" N THR C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.631A pdb=" N ARG D 189 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.628A pdb=" N TRP D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 259 through 298 removed outlier: 3.507A pdb=" N TYR D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 92 through 106 Processing helix chain 'E' and resid 109 through 134 Processing helix chain 'E' and resid 147 through 171 removed outlier: 4.141A pdb=" N GLN E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 188 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.644A pdb=" N VAL E 193 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 removed outlier: 4.290A pdb=" N PHE E 208 " --> pdb=" O GLY E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 224 Processing helix chain 'E' and resid 229 through 259 Processing helix chain 'E' and resid 261 through 265 Processing helix chain 'E' and resid 273 through 286 Processing helix chain 'E' and resid 297 through 327 removed outlier: 4.037A pdb=" N LEU E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY E 310 " --> pdb=" O PHE E 306 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 314 " --> pdb=" O GLY E 310 " (cutoff:3.500A) Proline residue: E 320 - end of helix Processing helix chain 'E' and resid 352 through 364 Processing helix chain 'E' and resid 384 through 394 Processing helix chain 'E' and resid 407 through 414 Processing helix chain 'E' and resid 432 through 451 Processing helix chain 'E' and resid 462 through 471 removed outlier: 3.571A pdb=" N LYS E 466 " --> pdb=" O GLN E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 500 Processing helix chain 'E' and resid 502 through 512 Processing helix chain 'E' and resid 523 through 533 removed outlier: 3.810A pdb=" N TYR E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 549 through 555 Processing helix chain 'E' and resid 556 through 562 Processing helix chain 'E' and resid 601 through 606 removed outlier: 3.509A pdb=" N LYS E 606 " --> pdb=" O ALA E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 704 removed outlier: 3.637A pdb=" N VAL E 703 " --> pdb=" O GLU E 699 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 713 Processing helix chain 'E' and resid 734 through 739 Processing helix chain 'E' and resid 759 through 771 removed outlier: 3.744A pdb=" N LEU E 763 " --> pdb=" O SER E 759 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 768 " --> pdb=" O LYS E 764 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR E 769 " --> pdb=" O ARG E 765 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 770 " --> pdb=" O GLU E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 792 removed outlier: 3.690A pdb=" N LEU E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 830 Processing helix chain 'E' and resid 872 through 876 removed outlier: 4.059A pdb=" N ASN E 875 " --> pdb=" O THR E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 887 through 892 removed outlier: 3.791A pdb=" N LEU E 891 " --> pdb=" O ASN E 887 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP E 892 " --> pdb=" O VAL E 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 887 through 892' Processing helix chain 'E' and resid 902 through 905 Processing helix chain 'E' and resid 906 through 911 Processing helix chain 'E' and resid 918 through 921 Processing helix chain 'E' and resid 922 through 930 Processing helix chain 'E' and resid 930 through 941 removed outlier: 4.264A pdb=" N LEU E 934 " --> pdb=" O ASN E 930 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 935 " --> pdb=" O ASP E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 957 Processing helix chain 'E' and resid 965 through 971 Processing helix chain 'E' and resid 986 through 994 removed outlier: 4.370A pdb=" N LEU E 990 " --> pdb=" O PRO E 986 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 994 " --> pdb=" O LEU E 990 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1008 removed outlier: 3.632A pdb=" N LEU E 999 " --> pdb=" O CYS E 995 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.712A pdb=" N LEU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 190 removed outlier: 3.786A pdb=" N ARG F 189 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 209 through 219 removed outlier: 3.537A pdb=" N ARG F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 229 removed outlier: 3.822A pdb=" N THR F 228 " --> pdb=" O SER F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 245 Processing helix chain 'F' and resid 247 through 251 Processing helix chain 'F' and resid 259 through 298 removed outlier: 3.822A pdb=" N ALA F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 22 through 49 Processing helix chain 'G' and resid 92 through 106 Processing helix chain 'G' and resid 109 through 134 Processing helix chain 'G' and resid 147 through 171 removed outlier: 3.791A pdb=" N GLN G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 179 removed outlier: 3.505A pdb=" N LEU G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 188 Processing helix chain 'G' and resid 189 through 200 removed outlier: 3.715A pdb=" N VAL G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 215 removed outlier: 4.538A pdb=" N PHE G 208 " --> pdb=" O GLY G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 224 Processing helix chain 'G' and resid 229 through 259 Processing helix chain 'G' and resid 261 through 265 Processing helix chain 'G' and resid 273 through 286 Processing helix chain 'G' and resid 297 through 327 removed outlier: 4.023A pdb=" N LEU G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY G 310 " --> pdb=" O PHE G 306 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA G 313 " --> pdb=" O LEU G 309 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET G 314 " --> pdb=" O GLY G 310 " (cutoff:3.500A) Proline residue: G 320 - end of helix Processing helix chain 'G' and resid 352 through 364 Processing helix chain 'G' and resid 384 through 394 Processing helix chain 'G' and resid 407 through 414 Processing helix chain 'G' and resid 432 through 451 Processing helix chain 'G' and resid 462 through 471 removed outlier: 3.663A pdb=" N LYS G 466 " --> pdb=" O GLN G 462 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN G 471 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 500 Processing helix chain 'G' and resid 502 through 512 Processing helix chain 'G' and resid 523 through 533 removed outlier: 4.311A pdb=" N TYR G 527 " --> pdb=" O THR G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 547 removed outlier: 3.929A pdb=" N GLY G 547 " --> pdb=" O ALA G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 555 removed outlier: 3.899A pdb=" N VAL G 553 " --> pdb=" O SER G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 562 Processing helix chain 'G' and resid 601 through 606 Processing helix chain 'G' and resid 699 through 704 removed outlier: 3.641A pdb=" N VAL G 703 " --> pdb=" O GLU G 699 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 713 Processing helix chain 'G' and resid 734 through 742 Proline residue: G 740 - end of helix Processing helix chain 'G' and resid 759 through 766 Processing helix chain 'G' and resid 785 through 792 removed outlier: 3.611A pdb=" N LEU G 789 " --> pdb=" O SER G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 793 through 797 removed outlier: 3.589A pdb=" N LEU G 796 " --> pdb=" O ASN G 793 " (cutoff:3.500A) Processing helix chain 'G' and resid 817 through 830 Processing helix chain 'G' and resid 872 through 876 removed outlier: 3.711A pdb=" N ASN G 875 " --> pdb=" O THR G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 884 through 891 removed outlier: 3.757A pdb=" N GLN G 889 " --> pdb=" O THR G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 906 through 911 Processing helix chain 'G' and resid 916 through 919 removed outlier: 3.783A pdb=" N VAL G 919 " --> pdb=" O ALA G 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 916 through 919' Processing helix chain 'G' and resid 920 through 930 removed outlier: 4.105A pdb=" N MET G 924 " --> pdb=" O LEU G 920 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER G 925 " --> pdb=" O ASP G 921 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR G 928 " --> pdb=" O MET G 924 " (cutoff:3.500A) Processing helix chain 'G' and resid 930 through 941 removed outlier: 3.976A pdb=" N LEU G 934 " --> pdb=" O ASN G 930 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR G 935 " --> pdb=" O ASP G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 946 through 957 Processing helix chain 'G' and resid 965 through 971 Processing helix chain 'G' and resid 987 through 994 removed outlier: 3.965A pdb=" N ASP G 992 " --> pdb=" O ALA G 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY G 993 " --> pdb=" O ASP G 989 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY G 994 " --> pdb=" O LEU G 990 " (cutoff:3.500A) Processing helix chain 'G' and resid 995 through 1007 removed outlier: 3.520A pdb=" N LEU G 999 " --> pdb=" O CYS G 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.638A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 209 through 219 removed outlier: 3.566A pdb=" N ARG H 218 " --> pdb=" O ALA H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 227 Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.501A pdb=" N SER H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 298 removed outlier: 3.814A pdb=" N ALA H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.588A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 537 through 540 Processing sheet with id=AA4, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.282A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 976 through 980 removed outlier: 3.978A pdb=" N PHE A1050 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.577A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 148 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.827A pdb=" N LEU B 86 " --> pdb=" O SER B 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.645A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 540 Processing sheet with id=AB2, first strand: chain 'C' and resid 776 through 780 removed outlier: 5.541A pdb=" N SER C 804 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 976 through 981 removed outlier: 3.921A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 48 through 50 removed outlier: 3.617A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA D 55 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU D 148 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 86 removed outlier: 4.091A pdb=" N LEU D 86 " --> pdb=" O SER D 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 139 through 140 Processing sheet with id=AB7, first strand: chain 'E' and resid 398 through 402 removed outlier: 4.464A pdb=" N GLY E 349 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA E 421 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN E 459 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE E 456 " --> pdb=" O ASP E 482 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE E 484 " --> pdb=" O ILE E 456 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR E 458 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 537 through 540 Processing sheet with id=AB9, first strand: chain 'E' and resid 776 through 780 removed outlier: 6.369A pdb=" N ILE E 754 " --> pdb=" O SER E 777 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU E 779 " --> pdb=" O ILE E 754 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE E 756 " --> pdb=" O LEU E 779 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER E 804 " --> pdb=" O GLU E 881 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE E 915 " --> pdb=" O ILE E 878 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR E 880 " --> pdb=" O PHE E 915 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 976 through 981 removed outlier: 4.247A pdb=" N GLY E1013 " --> pdb=" O PHE E1050 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 50 removed outlier: 3.656A pdb=" N LEU F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 148 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC4, first strand: chain 'G' and resid 139 through 140 Processing sheet with id=AC5, first strand: chain 'G' and resid 398 through 402 removed outlier: 3.540A pdb=" N HIS G 379 " --> pdb=" O TYR G 401 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY G 349 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU G 423 " --> pdb=" O HIS G 344 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL G 346 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU G 425 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS G 348 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN G 459 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE G 456 " --> pdb=" O ASP G 482 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE G 484 " --> pdb=" O ILE G 456 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR G 458 " --> pdb=" O ILE G 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 537 through 540 Processing sheet with id=AC7, first strand: chain 'G' and resid 776 through 780 removed outlier: 6.368A pdb=" N CYS G 800 " --> pdb=" O ILE G 879 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU G 881 " --> pdb=" O CYS G 800 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE G 802 " --> pdb=" O GLU G 881 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE G 915 " --> pdb=" O ILE G 878 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR G 880 " --> pdb=" O PHE G 915 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 976 through 981 removed outlier: 4.181A pdb=" N GLY G1013 " --> pdb=" O PHE G1050 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU G1052 " --> pdb=" O CYS G1011 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS G1011 " --> pdb=" O LEU G1052 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.081A pdb=" N LEU H 148 " --> pdb=" O SER H 173 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 85 through 86 removed outlier: 3.771A pdb=" N LEU H 86 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1566 hydrogen bonds defined for protein. 4392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6645 1.33 - 1.45: 9120 1.45 - 1.57: 20571 1.57 - 1.69: 0 1.69 - 1.81: 320 Bond restraints: 36656 Sorted by residual: bond pdb=" CA PRO C1037 " pdb=" C PRO C1037 " ideal model delta sigma weight residual 1.514 1.538 -0.024 5.50e-03 3.31e+04 1.93e+01 bond pdb=" N ASN C1036 " pdb=" CA ASN C1036 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.86e+01 bond pdb=" C PRO C1037 " pdb=" O PRO C1037 " ideal model delta sigma weight residual 1.246 1.213 0.033 8.50e-03 1.38e+04 1.47e+01 bond pdb=" N MET A 21 " pdb=" CA MET A 21 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.17e+01 bond pdb=" N TYR C1032 " pdb=" CA TYR C1032 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.16e-02 7.43e+03 1.06e+01 ... (remaining 36651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 48676 2.14 - 4.28: 1011 4.28 - 6.42: 117 6.42 - 8.56: 13 8.56 - 10.70: 3 Bond angle restraints: 49820 Sorted by residual: angle pdb=" C ASN C1036 " pdb=" CA ASN C1036 " pdb=" CB ASN C1036 " ideal model delta sigma weight residual 111.00 102.56 8.44 8.70e-01 1.32e+00 9.41e+01 angle pdb=" C ASP A 261 " pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " ideal model delta sigma weight residual 109.52 120.22 -10.70 1.58e+00 4.01e-01 4.59e+01 angle pdb=" C PHE C1012 " pdb=" CA PHE C1012 " pdb=" CB PHE C1012 " ideal model delta sigma weight residual 110.79 100.16 10.63 1.66e+00 3.63e-01 4.10e+01 angle pdb=" N ARG C 972 " pdb=" CA ARG C 972 " pdb=" C ARG C 972 " ideal model delta sigma weight residual 113.15 106.04 7.11 1.19e+00 7.06e-01 3.57e+01 angle pdb=" CA PHE C1000 " pdb=" CB PHE C1000 " pdb=" CG PHE C1000 " ideal model delta sigma weight residual 113.80 119.09 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 49815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 19608 18.14 - 36.27: 1802 36.27 - 54.41: 288 54.41 - 72.55: 42 72.55 - 90.69: 24 Dihedral angle restraints: 21764 sinusoidal: 8484 harmonic: 13280 Sorted by residual: dihedral pdb=" C PHE C1012 " pdb=" N PHE C1012 " pdb=" CA PHE C1012 " pdb=" CB PHE C1012 " ideal model delta harmonic sigma weight residual -122.60 -109.02 -13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" C PHE C1000 " pdb=" N PHE C1000 " pdb=" CA PHE C1000 " pdb=" CB PHE C1000 " ideal model delta harmonic sigma weight residual -122.60 -135.27 12.67 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" C ASP A 261 " pdb=" N ASP A 261 " pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " ideal model delta harmonic sigma weight residual -122.60 -134.93 12.33 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 21761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5259 0.079 - 0.158: 426 0.158 - 0.237: 46 0.237 - 0.316: 10 0.316 - 0.395: 3 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CA PHE C1012 " pdb=" N PHE C1012 " pdb=" C PHE C1012 " pdb=" CB PHE C1012 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA PHE C1000 " pdb=" N PHE C1000 " pdb=" C PHE C1000 " pdb=" CB PHE C1000 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA ASP A 261 " pdb=" N ASP A 261 " pdb=" C ASP A 261 " pdb=" CB ASP A 261 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 5741 not shown) Planarity restraints: 6296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 231 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C CYS B 231 " -0.070 2.00e-02 2.50e+03 pdb=" O CYS B 231 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL B 232 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 259 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C SER A 259 " 0.065 2.00e-02 2.50e+03 pdb=" O SER A 259 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 260 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 159 " 0.060 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO B 160 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 160 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 160 " 0.050 5.00e-02 4.00e+02 ... (remaining 6293 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 299 2.60 - 3.18: 30896 3.18 - 3.75: 55374 3.75 - 4.33: 76573 4.33 - 4.90: 126791 Nonbonded interactions: 289933 Sorted by model distance: nonbonded pdb=" OE2 GLU C 399 " pdb="MG MG C1101 " model vdw 2.029 2.170 nonbonded pdb=" CD2 PHE C 558 " pdb=" CE2 PHE C1000 " model vdw 2.086 3.640 nonbonded pdb=" NH1 ARG E 342 " pdb="MG MG E1101 " model vdw 2.090 2.250 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR E 290 " model vdw 2.113 3.040 nonbonded pdb=" OE2 GLU A 417 " pdb=" OH TYR A 450 " model vdw 2.114 3.040 ... (remaining 289928 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 1102) selection = chain 'C' selection = (chain 'E' and resid 13 through 1102) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.810 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 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: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36672 Z= 0.252 Angle : 0.696 10.699 49852 Z= 0.424 Chirality : 0.048 0.395 5744 Planarity : 0.005 0.091 6296 Dihedral : 14.002 90.685 13116 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.57 % Allowed : 1.03 % Favored : 98.41 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: 0.23 (0.12), residues: 4520 helix: 0.88 (0.12), residues: 1880 sheet: -0.08 (0.28), residues: 388 loop : -0.35 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 207 TYR 0.039 0.002 TYR G1015 PHE 0.027 0.002 PHE C1000 TRP 0.033 0.001 TRP C 93 HIS 0.007 0.001 HIS G 771 Details of bonding type rmsd covalent geometry : bond 0.00427 (36656) covalent geometry : angle 0.69620 (49820) SS BOND : bond 0.00357 ( 16) SS BOND : angle 0.51972 ( 32) hydrogen bonds : bond 0.15529 ( 1566) hydrogen bonds : angle 5.92222 ( 4392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 844 time to evaluate : 0.943 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 214 LEU cc_start: 0.8340 (tp) cc_final: 0.8091 (mp) REVERT: A 265 ASN cc_start: 0.6228 (m-40) cc_final: 0.5576 (t0) REVERT: A 420 ASP cc_start: 0.6179 (t70) cc_final: 0.5893 (t0) REVERT: A 763 LEU cc_start: 0.6942 (mm) cc_final: 0.6666 (mt) REVERT: A 830 MET cc_start: 0.7837 (mtp) cc_final: 0.7607 (mtt) REVERT: A 924 MET cc_start: 0.6367 (mtt) cc_final: 0.5525 (mtt) REVERT: C 257 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 332 TYR cc_start: 0.7118 (m-80) cc_final: 0.6627 (m-80) REVERT: C 361 LYS cc_start: 0.6978 (ptpt) cc_final: 0.6519 (pptt) REVERT: C 381 ILE cc_start: 0.7088 (mp) cc_final: 0.6881 (mt) REVERT: C 399 GLU cc_start: 0.6432 (mt-10) cc_final: 0.6096 (mt-10) REVERT: C 424 ILE cc_start: 0.8249 (mp) cc_final: 0.8014 (mt) REVERT: C 893 GLN cc_start: 0.4871 (mp10) cc_final: 0.3997 (mp10) REVERT: C 1027 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.5377 (mm-40) REVERT: C 1030 LYS cc_start: 0.7356 (mtpp) cc_final: 0.7035 (mtmm) REVERT: D 74 ARG cc_start: 0.3897 (mmt90) cc_final: 0.2951 (ttt180) REVERT: D 230 LEU cc_start: 0.4040 (mt) cc_final: 0.3810 (mp) REVERT: E 31 VAL cc_start: 0.6068 (p) cc_final: 0.5819 (m) REVERT: E 325 LEU cc_start: 0.7224 (tt) cc_final: 0.6924 (tt) REVERT: E 874 VAL cc_start: 0.6234 (p) cc_final: 0.6000 (m) REVERT: E 901 THR cc_start: 0.6049 (m) cc_final: 0.5727 (m) REVERT: E 904 TYR cc_start: 0.6722 (p90) cc_final: 0.6477 (p90) REVERT: F 237 LEU cc_start: 0.2150 (mt) cc_final: 0.1866 (mp) REVERT: G 154 MET cc_start: 0.7252 (mmm) cc_final: 0.6950 (tpt) REVERT: G 352 THR cc_start: 0.7874 (m) cc_final: 0.7654 (p) REVERT: G 420 ASP cc_start: 0.6682 (t70) cc_final: 0.6334 (t0) REVERT: G 470 LEU cc_start: 0.4754 (mm) cc_final: 0.4440 (mt) REVERT: G 551 PRO cc_start: 0.0936 (Cg_endo) cc_final: 0.0411 (Cg_exo) REVERT: G 578 ARG cc_start: 0.5045 (tpp-160) cc_final: 0.4097 (mmm160) REVERT: G 596 PHE cc_start: 0.6496 (m-80) cc_final: 0.6240 (m-80) REVERT: G 731 LEU cc_start: 0.6200 (mp) cc_final: 0.5701 (tt) REVERT: G 874 VAL cc_start: 0.6881 (p) cc_final: 0.6568 (m) REVERT: G 913 THR cc_start: 0.6920 (p) cc_final: 0.6603 (p) REVERT: G 1017 LEU cc_start: 0.7002 (mt) cc_final: 0.6583 (tp) REVERT: G 1050 PHE cc_start: 0.6841 (m-80) cc_final: 0.6455 (m-80) outliers start: 22 outliers final: 7 residues processed: 863 average time/residue: 0.2105 time to fit residues: 290.5857 Evaluate side-chains 539 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 531 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 979 GLN Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 239 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 365 HIS A 409 HIS A 509 ASN A 772 ASN A 907 GLN C 365 HIS C 465 ASN ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 887 ASN C 893 GLN C 979 GLN E 108 GLN E 222 GLN E 397 GLN ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS E 887 ASN ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN G 451 HIS ** G 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1021 HIS H 147 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.208574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.178678 restraints weight = 43564.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.179198 restraints weight = 101163.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.176978 restraints weight = 68623.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.176382 restraints weight = 48318.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.176757 restraints weight = 40225.531| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 36672 Z= 0.172 Angle : 0.643 10.160 49852 Z= 0.329 Chirality : 0.043 0.158 5744 Planarity : 0.005 0.078 6296 Dihedral : 4.455 67.541 4929 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.93 % Allowed : 9.98 % Favored : 88.09 % 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 aren not related in a simple way. whole: 0.22 (0.12), residues: 4520 helix: 0.93 (0.12), residues: 1916 sheet: -0.19 (0.27), residues: 432 loop : -0.40 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1031 TYR 0.025 0.002 TYR G1015 PHE 0.027 0.002 PHE C 746 TRP 0.024 0.002 TRP C 93 HIS 0.007 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00393 (36656) covalent geometry : angle 0.64308 (49820) SS BOND : bond 0.00164 ( 16) SS BOND : angle 0.51956 ( 32) hydrogen bonds : bond 0.04557 ( 1566) hydrogen bonds : angle 4.74491 ( 4392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 583 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7049 (mtm) cc_final: 0.6783 (mtp) REVERT: A 193 VAL cc_start: 0.8421 (p) cc_final: 0.8173 (m) REVERT: A 214 LEU cc_start: 0.8589 (tp) cc_final: 0.8272 (mp) REVERT: A 265 ASN cc_start: 0.5962 (m-40) cc_final: 0.5560 (t0) REVERT: A 321 GLU cc_start: 0.6712 (mt-10) cc_final: 0.6407 (mt-10) REVERT: A 402 GLN cc_start: 0.7373 (tt0) cc_final: 0.7165 (tt0) REVERT: A 420 ASP cc_start: 0.6406 (t70) cc_final: 0.6120 (t0) REVERT: A 437 ASP cc_start: 0.6045 (m-30) cc_final: 0.5641 (m-30) REVERT: A 441 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6791 (tp) REVERT: A 471 ASN cc_start: 0.6228 (m-40) cc_final: 0.5863 (m-40) REVERT: A 562 LYS cc_start: 0.6874 (mmtm) cc_final: 0.6495 (ttmm) REVERT: A 830 MET cc_start: 0.7865 (mtp) cc_final: 0.7484 (mtp) REVERT: A 884 ASN cc_start: 0.7949 (t0) cc_final: 0.7737 (t0) REVERT: A 925 SER cc_start: 0.8537 (m) cc_final: 0.7943 (t) REVERT: B 259 LEU cc_start: 0.4216 (tp) cc_final: 0.3955 (pt) REVERT: C 314 MET cc_start: 0.8081 (ttp) cc_final: 0.7781 (ttm) REVERT: C 332 TYR cc_start: 0.7585 (m-80) cc_final: 0.6835 (m-80) REVERT: C 361 LYS cc_start: 0.7452 (ptpt) cc_final: 0.6942 (pptt) REVERT: C 388 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6077 (mt-10) REVERT: C 442 MET cc_start: 0.5966 (tpt) cc_final: 0.5611 (tpp) REVERT: C 566 ILE cc_start: 0.7174 (mt) cc_final: 0.6948 (mt) REVERT: C 882 LEU cc_start: 0.8211 (mt) cc_final: 0.7863 (pp) REVERT: C 893 GLN cc_start: 0.5701 (OUTLIER) cc_final: 0.4936 (mp10) REVERT: C 930 ASN cc_start: 0.6330 (OUTLIER) cc_final: 0.6098 (p0) REVERT: C 955 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5719 (mp0) REVERT: C 990 LEU cc_start: 0.2739 (OUTLIER) cc_final: 0.1761 (mt) REVERT: C 1027 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5426 (mm-40) REVERT: C 1030 LYS cc_start: 0.7718 (mtpp) cc_final: 0.7349 (mtmm) REVERT: C 1053 MET cc_start: 0.3527 (ppp) cc_final: 0.2578 (ttp) REVERT: D 74 ARG cc_start: 0.4462 (mmt90) cc_final: 0.2901 (ttt180) REVERT: E 31 VAL cc_start: 0.6242 (p) cc_final: 0.5924 (m) REVERT: E 124 ILE cc_start: 0.8407 (mm) cc_final: 0.8040 (mt) REVERT: E 324 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6395 (pt0) REVERT: E 526 LYS cc_start: 0.6801 (ttpt) cc_final: 0.6417 (tttt) REVERT: E 790 ARG cc_start: 0.7280 (mtt-85) cc_final: 0.6904 (mtt-85) REVERT: G 331 LYS cc_start: 0.6362 (ptmm) cc_final: 0.5970 (pttt) REVERT: G 420 ASP cc_start: 0.6646 (t70) cc_final: 0.6335 (t0) REVERT: G 578 ARG cc_start: 0.5344 (tpp-160) cc_final: 0.4423 (mmm160) REVERT: G 731 LEU cc_start: 0.6291 (mp) cc_final: 0.5886 (tt) REVERT: G 796 LEU cc_start: 0.6974 (mt) cc_final: 0.6710 (mt) REVERT: G 826 ASN cc_start: 0.7501 (t0) cc_final: 0.7220 (t0) REVERT: G 892 ASP cc_start: 0.7209 (m-30) cc_final: 0.6985 (m-30) outliers start: 75 outliers final: 47 residues processed: 634 average time/residue: 0.2105 time to fit residues: 217.6058 Evaluate side-chains 528 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 476 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 893 GLN Chi-restraints excluded: chain C residue 930 ASN Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 246 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 214 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 348 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 293 optimal weight: 0.7980 chunk 329 optimal weight: 5.9990 chunk 408 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 GLN C 157 ASN C 268 ASN C 465 ASN C 468 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 ASN ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 267 GLN G 268 ASN G 496 GLN ** G 907 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 = 0.4212 r_free = 0.4212 target = 0.207752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.178171 restraints weight = 43420.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.177962 restraints weight = 103915.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.175453 restraints weight = 67209.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.174530 restraints weight = 53433.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.175123 restraints weight = 41012.067| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36672 Z= 0.114 Angle : 0.516 7.395 49852 Z= 0.265 Chirality : 0.039 0.192 5744 Planarity : 0.004 0.053 6296 Dihedral : 4.015 65.880 4920 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.11 % Allowed : 12.78 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 4520 helix: 1.20 (0.12), residues: 1920 sheet: -0.22 (0.27), residues: 432 loop : -0.37 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 972 TYR 0.022 0.001 TYR E 996 PHE 0.029 0.001 PHE E 558 TRP 0.015 0.001 TRP C 93 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00254 (36656) covalent geometry : angle 0.51614 (49820) SS BOND : bond 0.00171 ( 16) SS BOND : angle 0.41290 ( 32) hydrogen bonds : bond 0.04166 ( 1566) hydrogen bonds : angle 4.49553 ( 4392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 494 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7149 (mtm) cc_final: 0.6883 (mtp) REVERT: A 200 ASN cc_start: 0.6515 (m-40) cc_final: 0.5984 (m-40) REVERT: A 214 LEU cc_start: 0.8663 (tp) cc_final: 0.8286 (mp) REVERT: A 265 ASN cc_start: 0.5866 (m-40) cc_final: 0.5470 (t0) REVERT: A 339 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8141 (t) REVERT: A 420 ASP cc_start: 0.6444 (t70) cc_final: 0.6215 (t0) REVERT: A 441 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 456 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 471 ASN cc_start: 0.6051 (m-40) cc_final: 0.5533 (m-40) REVERT: A 562 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6402 (ttmm) REVERT: A 799 MET cc_start: 0.7577 (tpp) cc_final: 0.7330 (tpp) REVERT: B 141 PRO cc_start: 0.1491 (Cg_endo) cc_final: 0.1289 (Cg_exo) REVERT: B 166 LEU cc_start: 0.2641 (OUTLIER) cc_final: 0.1984 (mt) REVERT: B 170 ARG cc_start: 0.3593 (tpt90) cc_final: 0.3361 (tmt170) REVERT: B 209 LEU cc_start: 0.4124 (OUTLIER) cc_final: 0.3583 (mt) REVERT: B 259 LEU cc_start: 0.3958 (tp) cc_final: 0.3756 (pt) REVERT: C 94 MET cc_start: 0.6755 (mmt) cc_final: 0.6535 (tpp) REVERT: C 201 ARG cc_start: 0.5046 (OUTLIER) cc_final: 0.4602 (ttm-80) REVERT: C 314 MET cc_start: 0.7950 (ttp) cc_final: 0.7683 (ttm) REVERT: C 332 TYR cc_start: 0.7544 (m-80) cc_final: 0.6796 (m-80) REVERT: C 361 LYS cc_start: 0.7219 (ptpt) cc_final: 0.6825 (pptt) REVERT: C 388 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5989 (mt-10) REVERT: C 402 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7424 (tt0) REVERT: C 424 ILE cc_start: 0.8676 (mp) cc_final: 0.8397 (mt) REVERT: C 442 MET cc_start: 0.5992 (tpt) cc_final: 0.5776 (tpp) REVERT: C 739 MET cc_start: 0.5816 (mtt) cc_final: 0.5502 (mtm) REVERT: C 955 GLU cc_start: 0.6138 (mm-30) cc_final: 0.5773 (mp0) REVERT: C 1005 LYS cc_start: 0.5210 (mtpt) cc_final: 0.4950 (mttt) REVERT: C 1027 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5455 (mm-40) REVERT: C 1030 LYS cc_start: 0.7719 (mtpp) cc_final: 0.7386 (mtmm) REVERT: C 1053 MET cc_start: 0.3413 (ppp) cc_final: 0.3117 (ttp) REVERT: D 74 ARG cc_start: 0.4401 (mmt90) cc_final: 0.2845 (ttt180) REVERT: E 31 VAL cc_start: 0.6256 (p) cc_final: 0.5983 (m) REVERT: E 124 ILE cc_start: 0.8357 (mm) cc_final: 0.7972 (mt) REVERT: E 154 MET cc_start: 0.6954 (tpp) cc_final: 0.6656 (tpt) REVERT: E 513 MET cc_start: 0.7546 (mmt) cc_final: 0.6928 (mmt) REVERT: E 698 LYS cc_start: 0.7332 (mttp) cc_final: 0.6730 (mtpt) REVERT: E 739 MET cc_start: 0.6348 (ttp) cc_final: 0.6084 (ttp) REVERT: G 263 TRP cc_start: 0.7696 (p90) cc_final: 0.7467 (p90) REVERT: G 331 LYS cc_start: 0.6399 (ptmm) cc_final: 0.5971 (pttt) REVERT: G 420 ASP cc_start: 0.6734 (t70) cc_final: 0.6270 (t70) REVERT: G 578 ARG cc_start: 0.5303 (tpp-160) cc_final: 0.4308 (mmm160) REVERT: G 731 LEU cc_start: 0.6359 (mp) cc_final: 0.5909 (tt) REVERT: G 739 MET cc_start: 0.6557 (ttt) cc_final: 0.6352 (ttm) REVERT: G 907 GLN cc_start: 0.7485 (tt0) cc_final: 0.7193 (tt0) REVERT: G 996 TYR cc_start: 0.5398 (t80) cc_final: 0.4984 (t80) outliers start: 82 outliers final: 53 residues processed: 550 average time/residue: 0.1815 time to fit residues: 164.4642 Evaluate side-chains 505 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 444 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 201 ARG Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1015 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 734 LEU Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 246 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 281 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 434 optimal weight: 10.0000 chunk 340 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 429 optimal weight: 0.4980 chunk 149 optimal weight: 0.0060 chunk 120 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 173 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 HIS C 465 ASN C 468 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN G 826 ASN G 907 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.207023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.177104 restraints weight = 43185.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.176965 restraints weight = 102174.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174714 restraints weight = 69086.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.173840 restraints weight = 52656.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.174325 restraints weight = 41364.479| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 36672 Z= 0.103 Angle : 0.493 6.866 49852 Z= 0.253 Chirality : 0.039 0.192 5744 Planarity : 0.004 0.052 6296 Dihedral : 3.849 67.095 4920 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.57 % Allowed : 13.89 % Favored : 83.54 % 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 aren not related in a simple way. whole: 0.47 (0.13), residues: 4520 helix: 1.22 (0.12), residues: 1956 sheet: -0.21 (0.27), residues: 432 loop : -0.36 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 972 TYR 0.017 0.001 TYR G1015 PHE 0.018 0.001 PHE A 511 TRP 0.013 0.001 TRP C 477 HIS 0.010 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00224 (36656) covalent geometry : angle 0.49348 (49820) SS BOND : bond 0.00139 ( 16) SS BOND : angle 0.35243 ( 32) hydrogen bonds : bond 0.03720 ( 1566) hydrogen bonds : angle 4.33378 ( 4392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 471 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ARG cc_start: 0.7699 (mtt90) cc_final: 0.7445 (mtt-85) REVERT: A 214 LEU cc_start: 0.8694 (tp) cc_final: 0.8302 (mp) REVERT: A 265 ASN cc_start: 0.5851 (m-40) cc_final: 0.5532 (t0) REVERT: A 339 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8103 (t) REVERT: A 420 ASP cc_start: 0.6509 (t70) cc_final: 0.6244 (t0) REVERT: A 441 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6644 (tp) REVERT: A 456 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 562 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6477 (ttmm) REVERT: A 691 MET cc_start: 0.5235 (mmt) cc_final: 0.4868 (mmm) REVERT: A 706 THR cc_start: 0.6251 (OUTLIER) cc_final: 0.5868 (p) REVERT: A 764 LYS cc_start: 0.5621 (ttpt) cc_final: 0.4784 (mmtt) REVERT: A 778 ILE cc_start: 0.7657 (OUTLIER) cc_final: 0.7359 (mt) REVERT: B 141 PRO cc_start: 0.1420 (Cg_endo) cc_final: 0.1172 (Cg_exo) REVERT: B 166 LEU cc_start: 0.2626 (OUTLIER) cc_final: 0.1998 (mt) REVERT: B 170 ARG cc_start: 0.3670 (tpt90) cc_final: 0.3463 (tmt170) REVERT: B 209 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3499 (mt) REVERT: C 332 TYR cc_start: 0.7512 (m-80) cc_final: 0.6870 (m-80) REVERT: C 361 LYS cc_start: 0.7403 (ptpt) cc_final: 0.7007 (pptt) REVERT: C 402 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7532 (tt0) REVERT: C 442 MET cc_start: 0.6167 (tpt) cc_final: 0.5918 (tpp) REVERT: C 565 MET cc_start: 0.5892 (ttm) cc_final: 0.5369 (ttt) REVERT: C 739 MET cc_start: 0.5739 (mtt) cc_final: 0.5384 (mtm) REVERT: C 949 LEU cc_start: 0.7740 (tt) cc_final: 0.7319 (tt) REVERT: C 955 GLU cc_start: 0.6102 (mm-30) cc_final: 0.5818 (mp0) REVERT: C 976 ARG cc_start: 0.5282 (ptt180) cc_final: 0.4543 (ptt90) REVERT: C 1015 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6357 (t80) REVERT: C 1027 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.5344 (mm-40) REVERT: C 1030 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7389 (mtmm) REVERT: D 74 ARG cc_start: 0.4404 (mmt90) cc_final: 0.2721 (ttt180) REVERT: E 31 VAL cc_start: 0.6198 (p) cc_final: 0.5905 (m) REVERT: E 124 ILE cc_start: 0.8274 (mm) cc_final: 0.7866 (mt) REVERT: E 154 MET cc_start: 0.6891 (tpp) cc_final: 0.6596 (tpt) REVERT: E 324 GLU cc_start: 0.6691 (tm-30) cc_final: 0.5920 (tt0) REVERT: E 513 MET cc_start: 0.7512 (mmt) cc_final: 0.6865 (mmt) REVERT: E 698 LYS cc_start: 0.7282 (mttp) cc_final: 0.6702 (mtpt) REVERT: E 739 MET cc_start: 0.6367 (ttp) cc_final: 0.6040 (ttp) REVERT: F 123 LEU cc_start: 0.2175 (tp) cc_final: 0.1855 (tt) REVERT: G 154 MET cc_start: 0.7124 (mmm) cc_final: 0.6691 (tpt) REVERT: G 263 TRP cc_start: 0.7737 (p90) cc_final: 0.7523 (p90) REVERT: G 331 LYS cc_start: 0.6461 (ptmm) cc_final: 0.6016 (pttt) REVERT: G 420 ASP cc_start: 0.6858 (t70) cc_final: 0.6359 (t70) REVERT: G 486 LEU cc_start: 0.8270 (mm) cc_final: 0.7974 (mt) REVERT: G 578 ARG cc_start: 0.5240 (tpp-160) cc_final: 0.4260 (mmm160) REVERT: G 731 LEU cc_start: 0.6412 (mp) cc_final: 0.6126 (tp) REVERT: G 739 MET cc_start: 0.6654 (ttt) cc_final: 0.6428 (ttm) REVERT: G 933 ILE cc_start: 0.7559 (mm) cc_final: 0.7294 (mm) outliers start: 100 outliers final: 60 residues processed: 541 average time/residue: 0.1858 time to fit residues: 167.0437 Evaluate side-chains 498 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 428 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 826 ASN Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 982 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 163 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 324 optimal weight: 0.6980 chunk 289 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 331 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 979 GLN C 465 ASN C 468 HIS ** C 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 HIS E 525 GLN ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 402 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.202688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.171602 restraints weight = 43009.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.171809 restraints weight = 105805.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.169674 restraints weight = 67549.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.169034 restraints weight = 48508.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.169450 restraints weight = 38991.834| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36672 Z= 0.137 Angle : 0.524 7.095 49852 Z= 0.269 Chirality : 0.040 0.262 5744 Planarity : 0.004 0.053 6296 Dihedral : 3.938 67.593 4920 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 2.88 % Allowed : 15.20 % Favored : 81.92 % 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 aren not related in a simple way. whole: 0.40 (0.13), residues: 4520 helix: 1.21 (0.12), residues: 1952 sheet: -0.31 (0.27), residues: 432 loop : -0.44 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 201 TYR 0.025 0.002 TYR G 145 PHE 0.019 0.002 PHE E 558 TRP 0.013 0.001 TRP C 477 HIS 0.005 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00301 (36656) covalent geometry : angle 0.52365 (49820) SS BOND : bond 0.00176 ( 16) SS BOND : angle 0.39775 ( 32) hydrogen bonds : bond 0.04139 ( 1566) hydrogen bonds : angle 4.36961 ( 4392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 476 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 265 ASN cc_start: 0.5792 (m-40) cc_final: 0.5545 (t0) REVERT: A 373 VAL cc_start: 0.7909 (t) cc_final: 0.7524 (p) REVERT: A 420 ASP cc_start: 0.6516 (t70) cc_final: 0.6293 (t0) REVERT: A 440 ASN cc_start: 0.7861 (m-40) cc_final: 0.7389 (m-40) REVERT: A 456 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7983 (mt) REVERT: A 481 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7377 (t70) REVERT: A 562 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6443 (ttmm) REVERT: A 691 MET cc_start: 0.5761 (mmt) cc_final: 0.4899 (mmm) REVERT: A 706 THR cc_start: 0.6316 (OUTLIER) cc_final: 0.5935 (p) REVERT: A 764 LYS cc_start: 0.5636 (ttpt) cc_final: 0.4791 (mmtt) REVERT: A 778 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7541 (mm) REVERT: A 1053 MET cc_start: 0.4683 (ppp) cc_final: 0.4228 (ptm) REVERT: B 141 PRO cc_start: 0.1287 (Cg_endo) cc_final: 0.1033 (Cg_exo) REVERT: B 166 LEU cc_start: 0.2718 (OUTLIER) cc_final: 0.2055 (mt) REVERT: B 170 ARG cc_start: 0.3551 (tpt90) cc_final: 0.3335 (tmt170) REVERT: B 209 LEU cc_start: 0.3818 (OUTLIER) cc_final: 0.3578 (pp) REVERT: B 259 LEU cc_start: 0.4339 (tp) cc_final: 0.4085 (pt) REVERT: C 317 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7832 (p) REVERT: C 332 TYR cc_start: 0.7680 (m-80) cc_final: 0.6958 (m-80) REVERT: C 442 MET cc_start: 0.6189 (tpt) cc_final: 0.5982 (tpp) REVERT: C 565 MET cc_start: 0.5958 (ttm) cc_final: 0.5546 (ttt) REVERT: C 739 MET cc_start: 0.5823 (mtt) cc_final: 0.5558 (mtm) REVERT: C 949 LEU cc_start: 0.7628 (tt) cc_final: 0.7335 (tt) REVERT: C 955 GLU cc_start: 0.6237 (mm-30) cc_final: 0.5714 (mp0) REVERT: C 976 ARG cc_start: 0.5099 (ptt180) cc_final: 0.4592 (ptt-90) REVERT: C 1015 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6292 (t80) REVERT: C 1027 GLN cc_start: 0.5715 (OUTLIER) cc_final: 0.5328 (mm-40) REVERT: C 1030 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7496 (mtmm) REVERT: D 74 ARG cc_start: 0.4552 (mmt90) cc_final: 0.2688 (ttt180) REVERT: E 31 VAL cc_start: 0.6300 (p) cc_final: 0.6000 (m) REVERT: E 124 ILE cc_start: 0.8408 (mm) cc_final: 0.8040 (mt) REVERT: E 147 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6241 (p0) REVERT: E 154 MET cc_start: 0.6856 (tpp) cc_final: 0.6495 (tpt) REVERT: E 477 TRP cc_start: 0.4573 (p-90) cc_final: 0.4181 (p-90) REVERT: E 513 MET cc_start: 0.7745 (mmt) cc_final: 0.7034 (mmt) REVERT: E 698 LYS cc_start: 0.7319 (mttp) cc_final: 0.6738 (mtpt) REVERT: E 819 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5920 (mt-10) REVERT: E 907 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6820 (tm130) REVERT: F 123 LEU cc_start: 0.2429 (tp) cc_final: 0.2010 (tt) REVERT: G 30 MET cc_start: 0.6270 (ttp) cc_final: 0.6064 (mtm) REVERT: G 186 ASP cc_start: 0.7349 (m-30) cc_final: 0.7131 (m-30) REVERT: G 335 SER cc_start: 0.8150 (t) cc_final: 0.7915 (p) REVERT: G 460 MET cc_start: 0.6635 (mmp) cc_final: 0.6410 (mmp) REVERT: G 578 ARG cc_start: 0.5151 (tpp-160) cc_final: 0.4154 (mmm160) REVERT: G 691 MET cc_start: 0.6824 (mmp) cc_final: 0.6600 (mmm) REVERT: G 726 ASP cc_start: 0.4588 (m-30) cc_final: 0.4345 (m-30) outliers start: 112 outliers final: 79 residues processed: 557 average time/residue: 0.1899 time to fit residues: 173.4088 Evaluate side-chains 527 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 436 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 883 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 907 GLN Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 329 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 204 optimal weight: 0.0970 chunk 347 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 771 HIS ** C 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 ASN E 907 GLN G 402 GLN G 496 GLN ** G 745 ASN ** 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 = 0.4167 r_free = 0.4167 target = 0.203266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.171881 restraints weight = 42918.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.172428 restraints weight = 106933.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.171853 restraints weight = 72051.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.171388 restraints weight = 49940.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.171632 restraints weight = 43292.891| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36672 Z= 0.105 Angle : 0.494 7.693 49852 Z= 0.252 Chirality : 0.039 0.171 5744 Planarity : 0.004 0.053 6296 Dihedral : 3.826 68.379 4920 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 2.55 % Allowed : 16.54 % Favored : 80.92 % 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 aren not related in a simple way. whole: 0.50 (0.13), residues: 4520 helix: 1.32 (0.12), residues: 1956 sheet: -0.32 (0.27), residues: 432 loop : -0.39 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 17 TYR 0.016 0.001 TYR G 996 PHE 0.017 0.001 PHE E 558 TRP 0.027 0.001 TRP C 767 HIS 0.003 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00231 (36656) covalent geometry : angle 0.49425 (49820) SS BOND : bond 0.00152 ( 16) SS BOND : angle 0.34202 ( 32) hydrogen bonds : bond 0.03779 ( 1566) hydrogen bonds : angle 4.27838 ( 4392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 459 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6771 (mm) REVERT: A 265 ASN cc_start: 0.5790 (m-40) cc_final: 0.5561 (t0) REVERT: A 420 ASP cc_start: 0.6521 (t70) cc_final: 0.6298 (t0) REVERT: A 440 ASN cc_start: 0.7606 (m-40) cc_final: 0.7263 (m110) REVERT: A 456 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 562 LYS cc_start: 0.6920 (mmtm) cc_final: 0.6434 (ttmm) REVERT: A 691 MET cc_start: 0.5829 (mmt) cc_final: 0.5405 (mmm) REVERT: A 706 THR cc_start: 0.6305 (OUTLIER) cc_final: 0.5929 (p) REVERT: A 764 LYS cc_start: 0.5576 (ttpt) cc_final: 0.4740 (mmtt) REVERT: A 778 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7498 (mm) REVERT: A 987 PHE cc_start: 0.4232 (m-80) cc_final: 0.3917 (m-80) REVERT: A 996 TYR cc_start: 0.4138 (t80) cc_final: 0.3685 (t80) REVERT: A 1053 MET cc_start: 0.4740 (ppp) cc_final: 0.4247 (ptm) REVERT: B 141 PRO cc_start: 0.1539 (Cg_endo) cc_final: 0.1274 (Cg_exo) REVERT: B 166 LEU cc_start: 0.2642 (OUTLIER) cc_final: 0.1943 (mt) REVERT: B 182 LEU cc_start: 0.3554 (mt) cc_final: 0.2799 (tp) REVERT: B 209 LEU cc_start: 0.3892 (OUTLIER) cc_final: 0.3431 (mt) REVERT: C 317 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7683 (p) REVERT: C 332 TYR cc_start: 0.7674 (m-80) cc_final: 0.7007 (m-80) REVERT: C 565 MET cc_start: 0.5923 (ttm) cc_final: 0.5523 (ttt) REVERT: C 949 LEU cc_start: 0.7615 (tt) cc_final: 0.7271 (tt) REVERT: C 955 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5617 (mp0) REVERT: C 1015 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6329 (t80) REVERT: C 1024 THR cc_start: 0.6495 (OUTLIER) cc_final: 0.5878 (t) REVERT: C 1027 GLN cc_start: 0.5711 (OUTLIER) cc_final: 0.5335 (mm-40) REVERT: C 1030 LYS cc_start: 0.7814 (mtpp) cc_final: 0.7516 (mtmm) REVERT: D 74 ARG cc_start: 0.4542 (mmt90) cc_final: 0.2921 (ttm170) REVERT: E 31 VAL cc_start: 0.6288 (p) cc_final: 0.5995 (m) REVERT: E 124 ILE cc_start: 0.8329 (mm) cc_final: 0.8017 (mt) REVERT: E 145 TYR cc_start: 0.4503 (p90) cc_final: 0.4138 (p90) REVERT: E 147 ASP cc_start: 0.6463 (OUTLIER) cc_final: 0.6135 (p0) REVERT: E 154 MET cc_start: 0.6825 (tpp) cc_final: 0.6509 (tpt) REVERT: E 324 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6168 (tt0) REVERT: E 477 TRP cc_start: 0.4544 (p-90) cc_final: 0.4265 (p-90) REVERT: E 513 MET cc_start: 0.7738 (mmt) cc_final: 0.6887 (mmt) REVERT: E 698 LYS cc_start: 0.7322 (mttp) cc_final: 0.6757 (mtpt) REVERT: E 739 MET cc_start: 0.6413 (ttp) cc_final: 0.6059 (ttp) REVERT: E 819 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5980 (mt-10) REVERT: E 974 ARG cc_start: 0.6155 (ptt90) cc_final: 0.5922 (ptt-90) REVERT: F 123 LEU cc_start: 0.2396 (tp) cc_final: 0.1967 (tt) REVERT: F 210 ARG cc_start: 0.4136 (tpt-90) cc_final: 0.3714 (mmm160) REVERT: G 94 MET cc_start: 0.6092 (tpt) cc_final: 0.5835 (tpp) REVERT: G 186 ASP cc_start: 0.7478 (m-30) cc_final: 0.7233 (m-30) REVERT: G 335 SER cc_start: 0.8161 (t) cc_final: 0.7928 (p) REVERT: G 578 ARG cc_start: 0.5178 (tpp-160) cc_final: 0.4211 (mmm160) REVERT: G 739 MET cc_start: 0.6631 (ttt) cc_final: 0.6422 (ttm) REVERT: G 933 ILE cc_start: 0.7695 (mm) cc_final: 0.7396 (mm) REVERT: G 1051 CYS cc_start: 0.6076 (m) cc_final: 0.5605 (m) outliers start: 99 outliers final: 70 residues processed: 534 average time/residue: 0.1855 time to fit residues: 163.1068 Evaluate side-chains 510 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 429 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 793 ASN Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 883 VAL Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 124 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 281 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** C 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN E 534 ASN ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.202876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.171798 restraints weight = 42964.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.172686 restraints weight = 100337.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.171888 restraints weight = 68117.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.171518 restraints weight = 50275.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.171629 restraints weight = 43282.352| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36672 Z= 0.102 Angle : 0.490 12.107 49852 Z= 0.249 Chirality : 0.039 0.180 5744 Planarity : 0.004 0.054 6296 Dihedral : 3.766 70.059 4920 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 16.44 % Favored : 80.68 % 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 aren not related in a simple way. whole: 0.52 (0.13), residues: 4520 helix: 1.34 (0.12), residues: 1960 sheet: -0.32 (0.27), residues: 432 loop : -0.40 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 790 TYR 0.015 0.001 TYR G 996 PHE 0.015 0.001 PHE E 558 TRP 0.035 0.001 TRP C 767 HIS 0.003 0.001 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00227 (36656) covalent geometry : angle 0.49007 (49820) SS BOND : bond 0.00147 ( 16) SS BOND : angle 0.36312 ( 32) hydrogen bonds : bond 0.03700 ( 1566) hydrogen bonds : angle 4.24672 ( 4392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 452 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6668 (mm) REVERT: A 420 ASP cc_start: 0.6434 (t70) cc_final: 0.6217 (t0) REVERT: A 440 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7417 (m110) REVERT: A 456 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 481 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7421 (t70) REVERT: A 691 MET cc_start: 0.5875 (mmt) cc_final: 0.5436 (mmm) REVERT: A 706 THR cc_start: 0.6304 (OUTLIER) cc_final: 0.5937 (p) REVERT: A 764 LYS cc_start: 0.5475 (ttpt) cc_final: 0.4657 (mmtt) REVERT: A 778 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 987 PHE cc_start: 0.4259 (m-80) cc_final: 0.3950 (m-80) REVERT: A 996 TYR cc_start: 0.4186 (t80) cc_final: 0.3673 (t80) REVERT: A 1053 MET cc_start: 0.4758 (ppp) cc_final: 0.4283 (ptm) REVERT: B 141 PRO cc_start: 0.1641 (Cg_endo) cc_final: 0.1377 (Cg_exo) REVERT: B 166 LEU cc_start: 0.2566 (OUTLIER) cc_final: 0.1927 (mt) REVERT: B 182 LEU cc_start: 0.3365 (mt) cc_final: 0.2609 (tt) REVERT: B 209 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3779 (pp) REVERT: B 259 LEU cc_start: 0.4158 (tp) cc_final: 0.3942 (pt) REVERT: C 317 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7752 (p) REVERT: C 332 TYR cc_start: 0.7685 (m-80) cc_final: 0.7051 (m-80) REVERT: C 565 MET cc_start: 0.5860 (ttm) cc_final: 0.5523 (ttt) REVERT: C 949 LEU cc_start: 0.7650 (tt) cc_final: 0.7302 (tt) REVERT: C 1024 THR cc_start: 0.6513 (OUTLIER) cc_final: 0.5915 (t) REVERT: C 1027 GLN cc_start: 0.5720 (OUTLIER) cc_final: 0.5365 (mm-40) REVERT: C 1030 LYS cc_start: 0.7778 (mtpp) cc_final: 0.7499 (mtmm) REVERT: D 74 ARG cc_start: 0.4423 (mmt90) cc_final: 0.2884 (ttm170) REVERT: E 31 VAL cc_start: 0.6312 (OUTLIER) cc_final: 0.6013 (m) REVERT: E 46 LEU cc_start: 0.6554 (tt) cc_final: 0.6107 (mt) REVERT: E 124 ILE cc_start: 0.8304 (mm) cc_final: 0.7967 (mt) REVERT: E 154 MET cc_start: 0.6811 (tpp) cc_final: 0.6519 (tpt) REVERT: E 477 TRP cc_start: 0.4461 (p-90) cc_final: 0.4222 (p-90) REVERT: E 513 MET cc_start: 0.7701 (mmt) cc_final: 0.6843 (mmt) REVERT: E 605 VAL cc_start: 0.6575 (OUTLIER) cc_final: 0.6321 (t) REVERT: E 698 LYS cc_start: 0.7304 (mttp) cc_final: 0.6755 (mtpt) REVERT: E 739 MET cc_start: 0.6487 (ttp) cc_final: 0.6140 (ttp) REVERT: E 819 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5702 (mt-10) REVERT: E 907 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7109 (tm130) REVERT: F 123 LEU cc_start: 0.2019 (tp) cc_final: 0.1671 (tt) REVERT: F 210 ARG cc_start: 0.4009 (tpt-90) cc_final: 0.3572 (mmm160) REVERT: G 94 MET cc_start: 0.6070 (tpt) cc_final: 0.5844 (tpp) REVERT: G 186 ASP cc_start: 0.7529 (m-30) cc_final: 0.7278 (m-30) REVERT: G 335 SER cc_start: 0.8131 (t) cc_final: 0.7913 (p) REVERT: G 578 ARG cc_start: 0.5196 (tpp-160) cc_final: 0.4255 (mmm160) REVERT: G 739 MET cc_start: 0.6685 (ttt) cc_final: 0.6440 (ttm) REVERT: G 933 ILE cc_start: 0.7693 (mm) cc_final: 0.7450 (mm) REVERT: G 1051 CYS cc_start: 0.5971 (m) cc_final: 0.5762 (m) outliers start: 112 outliers final: 84 residues processed: 534 average time/residue: 0.1849 time to fit residues: 164.2910 Evaluate side-chains 523 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 424 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 819 GLU Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 907 GLN Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 977 VAL Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 156 optimal weight: 0.0370 chunk 375 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 406 optimal weight: 0.9980 chunk 256 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 377 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** E 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 402 GLN G 496 GLN ** G 745 ASN ** 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 = 0.4172 r_free = 0.4172 target = 0.203733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.161013 restraints weight = 42938.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.154975 restraints weight = 62663.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.155988 restraints weight = 61885.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.157834 restraints weight = 42270.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.157814 restraints weight = 36612.402| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36672 Z= 0.098 Angle : 0.486 10.660 49852 Z= 0.247 Chirality : 0.039 0.184 5744 Planarity : 0.004 0.054 6296 Dihedral : 3.704 71.849 4920 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 3.11 % Allowed : 16.67 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.13), residues: 4520 helix: 1.39 (0.12), residues: 1960 sheet: -0.25 (0.27), residues: 428 loop : -0.41 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 790 TYR 0.013 0.001 TYR G 996 PHE 0.014 0.001 PHE E 558 TRP 0.035 0.001 TRP C 767 HIS 0.003 0.001 HIS E 771 Details of bonding type rmsd covalent geometry : bond 0.00215 (36656) covalent geometry : angle 0.48583 (49820) SS BOND : bond 0.00141 ( 16) SS BOND : angle 0.34360 ( 32) hydrogen bonds : bond 0.03583 ( 1566) hydrogen bonds : angle 4.21061 ( 4392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 445 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.7717 (t80) cc_final: 0.7428 (t80) REVERT: A 150 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6629 (mm) REVERT: A 420 ASP cc_start: 0.6415 (t70) cc_final: 0.6199 (t0) REVERT: A 440 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7254 (m110) REVERT: A 456 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8061 (mt) REVERT: A 481 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7384 (t70) REVERT: A 691 MET cc_start: 0.5963 (mmt) cc_final: 0.5616 (mmm) REVERT: A 706 THR cc_start: 0.6438 (OUTLIER) cc_final: 0.5977 (p) REVERT: A 764 LYS cc_start: 0.6102 (ttpt) cc_final: 0.5062 (mmtt) REVERT: A 778 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7410 (mm) REVERT: A 996 TYR cc_start: 0.4684 (t80) cc_final: 0.4199 (t80) REVERT: A 1053 MET cc_start: 0.4736 (ppp) cc_final: 0.4396 (ptm) REVERT: B 166 LEU cc_start: 0.2895 (OUTLIER) cc_final: 0.2066 (mt) REVERT: B 182 LEU cc_start: 0.3368 (mt) cc_final: 0.2593 (tp) REVERT: B 259 LEU cc_start: 0.4219 (tp) cc_final: 0.3953 (pt) REVERT: C 332 TYR cc_start: 0.7736 (m-80) cc_final: 0.7102 (m-80) REVERT: C 565 MET cc_start: 0.6116 (ttm) cc_final: 0.5711 (ttt) REVERT: C 949 LEU cc_start: 0.7517 (tt) cc_final: 0.7146 (tt) REVERT: C 976 ARG cc_start: 0.5514 (ptt180) cc_final: 0.4882 (ptt90) REVERT: C 1015 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6235 (t80) REVERT: C 1024 THR cc_start: 0.6124 (OUTLIER) cc_final: 0.5754 (t) REVERT: C 1027 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.5209 (mm-40) REVERT: C 1030 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7319 (mtmm) REVERT: D 74 ARG cc_start: 0.5084 (mmt90) cc_final: 0.2900 (ttm170) REVERT: E 31 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6000 (m) REVERT: E 94 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.5674 (mpp) REVERT: E 124 ILE cc_start: 0.8302 (mm) cc_final: 0.7922 (mt) REVERT: E 154 MET cc_start: 0.6875 (tpp) cc_final: 0.6587 (tpt) REVERT: E 324 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6045 (tt0) REVERT: E 477 TRP cc_start: 0.4570 (p-90) cc_final: 0.4335 (p-90) REVERT: E 513 MET cc_start: 0.7725 (mmt) cc_final: 0.6809 (mmt) REVERT: E 605 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6380 (t) REVERT: E 698 LYS cc_start: 0.7129 (mttp) cc_final: 0.6551 (mtpt) REVERT: E 739 MET cc_start: 0.6537 (ttp) cc_final: 0.6222 (ttp) REVERT: E 907 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7297 (tm130) REVERT: F 123 LEU cc_start: 0.2799 (OUTLIER) cc_final: 0.2324 (tt) REVERT: F 210 ARG cc_start: 0.3715 (tpt-90) cc_final: 0.3309 (mmm160) REVERT: G 94 MET cc_start: 0.6302 (tpt) cc_final: 0.5887 (tpp) REVERT: G 186 ASP cc_start: 0.7531 (m-30) cc_final: 0.7308 (m-30) REVERT: G 214 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8323 (mp) REVERT: G 335 SER cc_start: 0.8198 (t) cc_final: 0.7960 (p) REVERT: G 578 ARG cc_start: 0.5206 (tpp-160) cc_final: 0.3586 (mtm180) REVERT: G 739 MET cc_start: 0.6739 (ttt) cc_final: 0.6434 (ttm) REVERT: G 933 ILE cc_start: 0.7770 (mm) cc_final: 0.7506 (mm) outliers start: 121 outliers final: 88 residues processed: 529 average time/residue: 0.2199 time to fit residues: 192.5137 Evaluate side-chains 530 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 426 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 907 GLN Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 883 VAL Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1017 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 201 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 436 optimal weight: 9.9990 chunk 419 optimal weight: 0.5980 chunk 374 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 428 optimal weight: 0.1980 chunk 99 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 884 ASN ** E 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.203503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.174247 restraints weight = 42818.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.170318 restraints weight = 100702.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.162585 restraints weight = 59608.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.162181 restraints weight = 58168.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.163300 restraints weight = 38472.248| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36672 Z= 0.101 Angle : 0.494 10.574 49852 Z= 0.249 Chirality : 0.039 0.196 5744 Planarity : 0.004 0.054 6296 Dihedral : 3.694 73.185 4920 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 2.96 % Allowed : 16.80 % Favored : 80.25 % 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 aren not related in a simple way. whole: 0.56 (0.13), residues: 4520 helix: 1.39 (0.12), residues: 1964 sheet: -0.26 (0.27), residues: 428 loop : -0.40 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 296 TYR 0.013 0.001 TYR G1015 PHE 0.023 0.001 PHE A 692 TRP 0.026 0.001 TRP C 767 HIS 0.003 0.001 HIS A 464 Details of bonding type rmsd covalent geometry : bond 0.00224 (36656) covalent geometry : angle 0.49417 (49820) SS BOND : bond 0.00151 ( 16) SS BOND : angle 0.35175 ( 32) hydrogen bonds : bond 0.03605 ( 1566) hydrogen bonds : angle 4.20362 ( 4392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 430 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.7739 (t80) cc_final: 0.7469 (t80) REVERT: A 150 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6660 (mm) REVERT: A 201 ARG cc_start: 0.5809 (ttm-80) cc_final: 0.5497 (ttm-80) REVERT: A 420 ASP cc_start: 0.6380 (t70) cc_final: 0.6166 (t0) REVERT: A 456 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 481 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7434 (t70) REVERT: A 691 MET cc_start: 0.5895 (mmt) cc_final: 0.5384 (mmm) REVERT: A 706 THR cc_start: 0.6348 (OUTLIER) cc_final: 0.5945 (p) REVERT: A 764 LYS cc_start: 0.5735 (ttpt) cc_final: 0.4743 (mmtt) REVERT: A 778 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7537 (mm) REVERT: A 996 TYR cc_start: 0.4406 (t80) cc_final: 0.3912 (t80) REVERT: A 1053 MET cc_start: 0.4791 (ppp) cc_final: 0.4393 (ptm) REVERT: B 166 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.1884 (mt) REVERT: B 182 LEU cc_start: 0.3383 (mt) cc_final: 0.2603 (tt) REVERT: C 332 TYR cc_start: 0.7737 (m-80) cc_final: 0.7111 (m-80) REVERT: C 442 MET cc_start: 0.6248 (tpp) cc_final: 0.6028 (tpp) REVERT: C 565 MET cc_start: 0.5903 (ttm) cc_final: 0.5476 (ttp) REVERT: C 949 LEU cc_start: 0.7775 (tt) cc_final: 0.7467 (tt) REVERT: C 1015 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6293 (t80) REVERT: C 1024 THR cc_start: 0.6355 (OUTLIER) cc_final: 0.5951 (t) REVERT: C 1027 GLN cc_start: 0.5694 (OUTLIER) cc_final: 0.5336 (mm-40) REVERT: C 1030 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7343 (mtmm) REVERT: D 74 ARG cc_start: 0.4801 (mmt90) cc_final: 0.2799 (ttm170) REVERT: E 31 VAL cc_start: 0.6356 (OUTLIER) cc_final: 0.6064 (m) REVERT: E 124 ILE cc_start: 0.8313 (mm) cc_final: 0.7929 (mt) REVERT: E 154 MET cc_start: 0.6821 (tpp) cc_final: 0.6554 (tpt) REVERT: E 324 GLU cc_start: 0.6833 (tm-30) cc_final: 0.6192 (tt0) REVERT: E 477 TRP cc_start: 0.4505 (p-90) cc_final: 0.4300 (p-90) REVERT: E 513 MET cc_start: 0.7728 (mmt) cc_final: 0.6824 (mmt) REVERT: E 605 VAL cc_start: 0.6728 (OUTLIER) cc_final: 0.6460 (t) REVERT: E 698 LYS cc_start: 0.7166 (mttp) cc_final: 0.6663 (mtpt) REVERT: E 739 MET cc_start: 0.6488 (ttp) cc_final: 0.6061 (ttt) REVERT: E 907 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7391 (tm130) REVERT: F 123 LEU cc_start: 0.2439 (OUTLIER) cc_final: 0.1986 (tt) REVERT: F 210 ARG cc_start: 0.3818 (tpt-90) cc_final: 0.3430 (mmm160) REVERT: G 186 ASP cc_start: 0.7560 (m-30) cc_final: 0.7308 (m-30) REVERT: G 214 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8310 (mp) REVERT: G 331 LYS cc_start: 0.6345 (ptmm) cc_final: 0.5901 (pttt) REVERT: G 335 SER cc_start: 0.8165 (t) cc_final: 0.7942 (p) REVERT: G 402 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: G 578 ARG cc_start: 0.5137 (tpp-160) cc_final: 0.3784 (mtm180) REVERT: G 739 MET cc_start: 0.6656 (ttt) cc_final: 0.6395 (ttm) REVERT: G 818 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7466 (mptt) REVERT: G 933 ILE cc_start: 0.7806 (mm) cc_final: 0.7552 (mm) REVERT: G 1012 PHE cc_start: 0.7263 (m-80) cc_final: 0.6818 (m-80) outliers start: 115 outliers final: 91 residues processed: 512 average time/residue: 0.2262 time to fit residues: 189.1410 Evaluate side-chains 528 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 422 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 907 GLN Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 402 GLN Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 20 optimal weight: 2.9990 chunk 382 optimal weight: 0.0020 chunk 285 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 425 optimal weight: 0.2980 chunk 395 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 771 HIS A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C 884 ASN E 468 HIS ** E 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 887 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.203190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.172735 restraints weight = 43038.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173330 restraints weight = 104459.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.171605 restraints weight = 66271.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.170918 restraints weight = 49201.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.171343 restraints weight = 39285.539| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36672 Z= 0.096 Angle : 0.484 10.522 49852 Z= 0.244 Chirality : 0.039 0.220 5744 Planarity : 0.004 0.054 6296 Dihedral : 3.651 75.804 4920 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 2.73 % Allowed : 17.08 % Favored : 80.20 % 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 aren not related in a simple way. whole: 0.61 (0.13), residues: 4520 helix: 1.43 (0.12), residues: 1964 sheet: -0.23 (0.27), residues: 428 loop : -0.37 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 296 TYR 0.015 0.001 TYR G 996 PHE 0.019 0.001 PHE A 692 TRP 0.040 0.001 TRP C 767 HIS 0.007 0.001 HIS A 771 Details of bonding type rmsd covalent geometry : bond 0.00208 (36656) covalent geometry : angle 0.48453 (49820) SS BOND : bond 0.00137 ( 16) SS BOND : angle 0.35087 ( 32) hydrogen bonds : bond 0.03485 ( 1566) hydrogen bonds : angle 4.16927 ( 4392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 446 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 PHE cc_start: 0.7729 (t80) cc_final: 0.7478 (t80) REVERT: A 133 ASP cc_start: 0.7133 (m-30) cc_final: 0.6661 (m-30) REVERT: A 321 GLU cc_start: 0.6558 (mt-10) cc_final: 0.6205 (mt-10) REVERT: A 420 ASP cc_start: 0.6470 (t70) cc_final: 0.6242 (t0) REVERT: A 456 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8095 (mt) REVERT: A 481 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7367 (t70) REVERT: A 691 MET cc_start: 0.5855 (mmt) cc_final: 0.5325 (mmm) REVERT: A 706 THR cc_start: 0.6300 (OUTLIER) cc_final: 0.5930 (p) REVERT: A 764 LYS cc_start: 0.5723 (ttpt) cc_final: 0.4689 (mmtt) REVERT: A 778 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7583 (mm) REVERT: A 996 TYR cc_start: 0.4256 (t80) cc_final: 0.3644 (t80) REVERT: A 1053 MET cc_start: 0.4953 (ppp) cc_final: 0.4515 (ptm) REVERT: B 166 LEU cc_start: 0.2604 (OUTLIER) cc_final: 0.2076 (mp) REVERT: B 182 LEU cc_start: 0.3478 (mt) cc_final: 0.2619 (tp) REVERT: C 47 LYS cc_start: 0.4760 (ttpt) cc_final: 0.4320 (mmtp) REVERT: C 332 TYR cc_start: 0.7715 (m-80) cc_final: 0.7096 (m-80) REVERT: C 442 MET cc_start: 0.6187 (tpp) cc_final: 0.5791 (tpp) REVERT: C 565 MET cc_start: 0.5830 (ttm) cc_final: 0.5406 (ttt) REVERT: C 949 LEU cc_start: 0.7828 (tt) cc_final: 0.7546 (tt) REVERT: C 976 ARG cc_start: 0.5701 (ptt-90) cc_final: 0.5002 (ptt-90) REVERT: C 1015 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6262 (t80) REVERT: C 1024 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6148 (t) REVERT: C 1027 GLN cc_start: 0.5708 (OUTLIER) cc_final: 0.5394 (mm110) REVERT: C 1030 LYS cc_start: 0.7578 (mtpp) cc_final: 0.7356 (mtmm) REVERT: C 1053 MET cc_start: 0.4249 (mtt) cc_final: 0.3807 (mtt) REVERT: D 74 ARG cc_start: 0.4468 (mmt90) cc_final: 0.2769 (ttm170) REVERT: E 94 MET cc_start: 0.5697 (mpp) cc_final: 0.5388 (mpp) REVERT: E 154 MET cc_start: 0.6744 (tpp) cc_final: 0.6467 (tpt) REVERT: E 324 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6294 (tt0) REVERT: E 605 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.6439 (t) REVERT: E 698 LYS cc_start: 0.7169 (mttp) cc_final: 0.6683 (mtpt) REVERT: E 907 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7584 (tm130) REVERT: F 123 LEU cc_start: 0.2092 (OUTLIER) cc_final: 0.1741 (tt) REVERT: F 189 ARG cc_start: 0.2711 (mtm180) cc_final: 0.2356 (mtm-85) REVERT: F 210 ARG cc_start: 0.3945 (tpt-90) cc_final: 0.3554 (mmm160) REVERT: G 186 ASP cc_start: 0.7514 (m-30) cc_final: 0.7225 (m-30) REVERT: G 214 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8267 (mp) REVERT: G 331 LYS cc_start: 0.6336 (ptmm) cc_final: 0.5850 (pttm) REVERT: G 486 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7979 (mt) REVERT: G 578 ARG cc_start: 0.5067 (tpp-160) cc_final: 0.3880 (mtm180) REVERT: G 582 ASN cc_start: 0.5152 (m-40) cc_final: 0.4677 (m-40) REVERT: G 739 MET cc_start: 0.6641 (ttt) cc_final: 0.6416 (ttm) REVERT: G 933 ILE cc_start: 0.7818 (mm) cc_final: 0.7577 (mm) outliers start: 106 outliers final: 86 residues processed: 519 average time/residue: 0.2206 time to fit residues: 188.5647 Evaluate side-chains 528 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 429 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1023 SER Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 722 CYS Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 907 GLN Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1017 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 264 GLU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 498 CYS Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 922 SER Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1046 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 251 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 444 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 325 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 ASN ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS C1054 GLN E 468 HIS ** E 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN ** G 745 ASN ** 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 = 0.4162 r_free = 0.4162 target = 0.202712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.160635 restraints weight = 42751.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.154127 restraints weight = 59215.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.154986 restraints weight = 61955.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.156861 restraints weight = 41574.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.157867 restraints weight = 32351.697| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36672 Z= 0.103 Angle : 0.499 11.641 49852 Z= 0.251 Chirality : 0.039 0.197 5744 Planarity : 0.004 0.054 6296 Dihedral : 3.679 77.387 4920 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 2.75 % Allowed : 17.28 % Favored : 79.96 % 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 aren not related in a simple way. whole: 0.61 (0.13), residues: 4520 helix: 1.43 (0.12), residues: 1964 sheet: -0.26 (0.27), residues: 428 loop : -0.38 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 296 TYR 0.019 0.001 TYR G 996 PHE 0.019 0.001 PHE A 692 TRP 0.030 0.001 TRP E 477 HIS 0.005 0.001 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00229 (36656) covalent geometry : angle 0.49942 (49820) SS BOND : bond 0.00148 ( 16) SS BOND : angle 0.37111 ( 32) hydrogen bonds : bond 0.03605 ( 1566) hydrogen bonds : angle 4.18411 ( 4392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5508.67 seconds wall clock time: 96 minutes 0.98 seconds (5760.98 seconds total)