Starting phenix.real_space_refine on Mon Jul 6 13:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynz_33976/07_2026/7ynz_33976.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynz_33976/07_2026/7ynz_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_33976/07_2026/7ynz_33976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynz_33976/07_2026/7ynz_33976.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynz_33976/07_2026/7ynz_33976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynz_33976/07_2026/7ynz_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-dev-6108/lib/python3.11/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, 1 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 1 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 7.50, per 1000 atoms: 0.21 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: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.50 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: 7.89 Time building geometry restraints manager: 4.17 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: 0.04 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.850 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.210 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:2.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 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 are 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/Z covalent geometry : bond 0.00427 / 0.25 (36656) covalent geometry : angle 0.69620 / 0.42 (49820) SS BOND : bond 0.00357 / 0.22 ( 16) SS BOND : angle 0.51972 / 0.31 ( 32) hydrogen bonds : bond 0.15529 / 10.10 ( 1566) hydrogen bonds : angle 5.92222 / 4.32 ( 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 : 1.426 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: 0.7606 (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: 0.6628 (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: 0.3996 (mp10) REVERT: C 1027 GLN cc_start: 0.5813 (OUTLIER) cc_final: 0.5378 (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: 0.6478 (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: 0.6333 (t0) REVERT: G 470 LEU cc_start: 0.4754 (mm) cc_final: 0.4442 (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: 0.4098 (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: 0.5700 (tt) REVERT: G 874 VAL cc_start: 0.6881 (p) cc_final: 0.6571 (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: 0.2403 time to fit residues: 332.7395 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 : 1.315 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 509 ASN A 772 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN C 365 HIS C 465 ASN ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 887 ASN ** E 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN G 451 HIS ** G 745 ASN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.205991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.175508 restraints weight = 43592.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.175753 restraints weight = 104267.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.174479 restraints weight = 70585.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.173781 restraints weight = 51630.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.174224 restraints weight = 41563.048| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 36672 Z= 0.191 Angle : 0.676 9.866 49852 Z= 0.347 Chirality : 0.045 0.175 5744 Planarity : 0.006 0.084 6296 Dihedral : 4.554 67.693 4929 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.98 % Allowed : 10.24 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4520 helix: 0.86 (0.12), residues: 1912 sheet: -0.24 (0.27), residues: 432 loop : -0.43 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 976 TYR 0.044 0.002 TYR C1039 PHE 0.025 0.002 PHE A1000 TRP 0.024 0.002 TRP C 93 HIS 0.008 0.002 HIS E 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (36656) covalent geometry : angle 0.67622 / 0.35 (49820) SS BOND : bond 0.00211 / 0.14 ( 16) SS BOND : angle 0.52643 / 0.33 ( 32) hydrogen bonds : bond 0.04941 / 3.26 ( 1566) hydrogen bonds : angle 4.82709 / 3.49 ( 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 657 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 580 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7010 (mtm) cc_final: 0.6742 (mtp) REVERT: A 265 ASN cc_start: 0.5975 (m-40) cc_final: 0.5550 (t0) REVERT: A 321 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6465 (mt-10) REVERT: A 420 ASP cc_start: 0.6379 (t70) cc_final: 0.6136 (t0) REVERT: A 437 ASP cc_start: 0.6174 (m-30) cc_final: 0.5705 (m-30) REVERT: A 441 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6769 (tp) REVERT: A 456 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 471 ASN cc_start: 0.6226 (m-40) cc_final: 0.5595 (m-40) REVERT: A 562 LYS cc_start: 0.6849 (mmtm) cc_final: 0.6498 (ttmm) REVERT: A 884 ASN cc_start: 0.8006 (t0) cc_final: 0.7795 (t0) REVERT: A 925 SER cc_start: 0.8558 (m) cc_final: 0.8015 (t) REVERT: A 1018 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.6348 (ttp80) REVERT: B 259 LEU cc_start: 0.4453 (tp) cc_final: 0.4172 (pt) REVERT: C 314 MET cc_start: 0.8080 (ttp) cc_final: 0.7776 (ttm) REVERT: C 332 TYR cc_start: 0.7657 (m-80) cc_final: 0.6904 (m-80) REVERT: C 361 LYS cc_start: 0.7480 (ptpt) cc_final: 0.6970 (pptt) REVERT: C 388 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6070 (mt-10) REVERT: C 442 MET cc_start: 0.6126 (tpt) cc_final: 0.5817 (tpp) REVERT: C 712 MET cc_start: 0.5474 (mtm) cc_final: 0.5274 (ppp) REVERT: C 893 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5202 (mp10) REVERT: C 955 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5646 (mp0) REVERT: C 990 LEU cc_start: 0.2896 (OUTLIER) cc_final: 0.2156 (mt) REVERT: C 999 LEU cc_start: 0.7026 (tt) cc_final: 0.6812 (tp) REVERT: C 1027 GLN cc_start: 0.5882 (OUTLIER) cc_final: 0.5522 (mm-40) REVERT: C 1030 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7354 (mtmm) REVERT: C 1053 MET cc_start: 0.3625 (ppp) cc_final: 0.2601 (ttp) REVERT: D 74 ARG cc_start: 0.4449 (mmt90) cc_final: 0.2907 (ttt180) REVERT: D 230 LEU cc_start: 0.4303 (mt) cc_final: 0.3931 (mt) REVERT: E 31 VAL cc_start: 0.6226 (p) cc_final: 0.5911 (m) REVERT: E 124 ILE cc_start: 0.8446 (mm) cc_final: 0.8109 (mt) REVERT: E 526 LYS cc_start: 0.6766 (ttpt) cc_final: 0.6477 (tttt) REVERT: E 1039 TYR cc_start: 0.4896 (t80) cc_final: 0.4689 (t80) REVERT: G 331 LYS cc_start: 0.6366 (ptmm) cc_final: 0.5977 (pttt) REVERT: G 578 ARG cc_start: 0.5346 (tpp-160) cc_final: 0.4428 (mmm160) REVERT: G 731 LEU cc_start: 0.6418 (mp) cc_final: 0.5990 (tt) REVERT: G 796 LEU cc_start: 0.7004 (mt) cc_final: 0.6724 (mt) REVERT: G 826 ASN cc_start: 0.7528 (t0) cc_final: 0.7250 (t0) outliers start: 77 outliers final: 50 residues processed: 635 average time/residue: 0.2290 time to fit residues: 237.7328 Evaluate side-chains 518 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 463 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 456 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 941 VAL 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 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 703 VAL 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 949 LEU Chi-restraints excluded: chain C residue 968 THR 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 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 734 LEU 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: 0.9990 chunk 65 optimal weight: 1.9990 chunk 348 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 408 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 ASN C 465 ASN C 468 HIS ** C 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 ASN ** E 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN E 907 GLN 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 = 0.4174 r_free = 0.4174 target = 0.203953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.172959 restraints weight = 43274.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.173489 restraints weight = 106019.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173191 restraints weight = 71974.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.172708 restraints weight = 51559.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.172946 restraints weight = 44554.099| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36672 Z= 0.135 Angle : 0.546 7.138 49852 Z= 0.280 Chirality : 0.040 0.199 5744 Planarity : 0.005 0.055 6296 Dihedral : 4.177 64.882 4921 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 13.19 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.13), residues: 4520 helix: 1.07 (0.12), residues: 1920 sheet: -0.30 (0.27), residues: 432 loop : -0.45 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 742 TYR 0.020 0.001 TYR G1015 PHE 0.035 0.002 PHE E 558 TRP 0.014 0.001 TRP C 93 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (36656) covalent geometry : angle 0.54614 / 0.28 (49820) SS BOND : bond 0.00192 / 0.13 ( 16) SS BOND : angle 0.41346 / 0.24 ( 32) hydrogen bonds : bond 0.04552 / 2.97 ( 1566) hydrogen bonds : angle 4.57849 / 3.31 ( 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 575 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 484 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.5328 (m110) cc_final: 0.5121 (m-40) REVERT: A 265 ASN cc_start: 0.5830 (m-40) cc_final: 0.5518 (t0) REVERT: A 339 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 373 VAL cc_start: 0.7582 (t) cc_final: 0.7206 (p) REVERT: A 374 GLU cc_start: 0.7129 (tt0) cc_final: 0.6889 (tt0) REVERT: A 420 ASP cc_start: 0.6518 (t70) cc_final: 0.6229 (t0) REVERT: A 441 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 562 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6399 (ttmm) REVERT: A 706 THR cc_start: 0.6262 (OUTLIER) cc_final: 0.5916 (p) REVERT: A 778 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7469 (mt) REVERT: A 799 MET cc_start: 0.7647 (tpp) cc_final: 0.7341 (tpp) REVERT: B 166 LEU cc_start: 0.2509 (OUTLIER) cc_final: 0.1836 (mm) REVERT: B 209 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3588 (mt) REVERT: C 201 ARG cc_start: 0.5273 (OUTLIER) cc_final: 0.4451 (mtm-85) REVERT: C 314 MET cc_start: 0.7992 (ttp) cc_final: 0.7747 (ttm) REVERT: C 332 TYR cc_start: 0.7626 (m-80) cc_final: 0.6924 (m-80) REVERT: C 361 LYS cc_start: 0.7396 (ptpt) cc_final: 0.7120 (pptt) REVERT: C 402 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7685 (tt0) REVERT: C 424 ILE cc_start: 0.8750 (mp) cc_final: 0.8528 (mt) REVERT: C 442 MET cc_start: 0.6069 (tpt) cc_final: 0.5828 (tpp) REVERT: C 739 MET cc_start: 0.5856 (mtt) cc_final: 0.5398 (mtm) REVERT: C 893 GLN cc_start: 0.6186 (mp10) cc_final: 0.5270 (mp10) REVERT: C 955 GLU cc_start: 0.6085 (mm-30) cc_final: 0.5749 (mp0) REVERT: C 1027 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.5435 (mm-40) REVERT: C 1030 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7454 (mtmm) REVERT: C 1053 MET cc_start: 0.3473 (ppp) cc_final: 0.2946 (ttp) REVERT: D 74 ARG cc_start: 0.4362 (mmt90) cc_final: 0.2933 (ttt180) REVERT: E 31 VAL cc_start: 0.6200 (p) cc_final: 0.5932 (m) REVERT: E 124 ILE cc_start: 0.8427 (mm) cc_final: 0.8082 (mt) REVERT: E 154 MET cc_start: 0.6971 (tpp) cc_final: 0.6586 (tpt) REVERT: E 417 GLU cc_start: 0.6535 (mp0) cc_final: 0.6300 (mp0) REVERT: E 477 TRP cc_start: 0.4522 (p-90) cc_final: 0.4184 (p-90) REVERT: E 513 MET cc_start: 0.7726 (mmt) cc_final: 0.7031 (mmt) REVERT: E 739 MET cc_start: 0.6521 (ttp) cc_final: 0.6162 (ttp) REVERT: G 331 LYS cc_start: 0.6381 (ptmm) cc_final: 0.5937 (pttt) REVERT: G 578 ARG cc_start: 0.5375 (tpp-160) cc_final: 0.4402 (mmm160) REVERT: G 731 LEU cc_start: 0.6518 (mp) cc_final: 0.6132 (tp) REVERT: H 113 ARG cc_start: 0.1716 (mmp-170) cc_final: 0.1510 (mmm160) outliers start: 91 outliers final: 63 residues processed: 548 average time/residue: 0.2245 time to fit residues: 202.0922 Evaluate side-chains 510 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 438 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 441 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 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 201 ARG 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 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 116 VAL Chi-restraints excluded: chain E residue 324 GLU 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 1033 VAL 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 293 VAL Chi-restraints excluded: chain G residue 373 VAL Chi-restraints excluded: chain G residue 416 ILE 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 794 ILE 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 243 THR 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: 0.0040 chunk 258 optimal weight: 2.9990 chunk 434 optimal weight: 0.3980 chunk 340 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 429 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 GLN A 979 GLN C 451 HIS C 468 HIS C 930 ASN E 409 HIS E 907 GLN G 402 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.201384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.170948 restraints weight = 43024.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.171104 restraints weight = 107011.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.169183 restraints weight = 69133.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.168269 restraints weight = 54486.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.168730 restraints weight = 42105.663| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36672 Z= 0.149 Angle : 0.578 6.747 49852 Z= 0.295 Chirality : 0.041 0.189 5744 Planarity : 0.005 0.055 6296 Dihedral : 4.259 65.546 4921 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.52 % Allowed : 14.38 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4520 helix: 0.98 (0.12), residues: 1936 sheet: -0.20 (0.27), residues: 412 loop : -0.50 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 742 TYR 0.019 0.002 TYR G1015 PHE 0.022 0.002 PHE C1000 TRP 0.012 0.001 TRP D 203 HIS 0.006 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (36656) covalent geometry : angle 0.57798 / 0.29 (49820) SS BOND : bond 0.00208 / 0.14 ( 16) SS BOND : angle 0.47918 / 0.30 ( 32) hydrogen bonds : bond 0.04493 / 2.95 ( 1566) hydrogen bonds : angle 4.56458 / 3.30 ( 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 624 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 487 time to evaluate : 1.042 Fit side-chains REVERT: A 151 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.5623 (pt0) REVERT: A 200 ASN cc_start: 0.5503 (m110) cc_final: 0.5280 (m-40) REVERT: A 201 ARG cc_start: 0.6186 (ttm-80) cc_final: 0.5972 (ttm-80) REVERT: A 265 ASN cc_start: 0.5828 (m-40) cc_final: 0.5561 (t0) REVERT: A 321 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6348 (mt-10) REVERT: A 339 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8084 (t) REVERT: A 373 VAL cc_start: 0.7982 (t) cc_final: 0.7620 (p) REVERT: A 420 ASP cc_start: 0.6508 (t70) cc_final: 0.6257 (t0) REVERT: A 456 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 481 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7674 (t0) REVERT: A 562 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6489 (ttmm) REVERT: A 706 THR cc_start: 0.6321 (OUTLIER) cc_final: 0.5969 (p) REVERT: A 778 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7629 (mm) REVERT: A 979 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5947 (tp40) REVERT: B 166 LEU cc_start: 0.2727 (OUTLIER) cc_final: 0.1911 (mt) REVERT: B 182 LEU cc_start: 0.3788 (mt) cc_final: 0.3318 (tp) REVERT: B 209 LEU cc_start: 0.3923 (OUTLIER) cc_final: 0.3380 (mt) REVERT: C 314 MET cc_start: 0.8035 (ttp) cc_final: 0.7757 (ttm) REVERT: C 933 ILE cc_start: 0.8068 (mm) cc_final: 0.7805 (mt) REVERT: C 949 LEU cc_start: 0.7751 (tt) cc_final: 0.7441 (tt) REVERT: C 955 GLU cc_start: 0.6111 (mm-30) cc_final: 0.5731 (mp0) REVERT: C 976 ARG cc_start: 0.5702 (ptt180) cc_final: 0.4838 (ptt90) REVERT: C 990 LEU cc_start: 0.2568 (OUTLIER) cc_final: 0.2021 (mt) REVERT: C 1027 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.5350 (mm-40) REVERT: C 1030 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7491 (mtmm) REVERT: D 74 ARG cc_start: 0.4509 (mmt90) cc_final: 0.2885 (ttm170) REVERT: E 31 VAL cc_start: 0.6246 (OUTLIER) cc_final: 0.5941 (m) REVERT: E 124 ILE cc_start: 0.8351 (mm) cc_final: 0.8115 (mt) REVERT: E 147 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.6365 (p0) REVERT: E 407 ASN cc_start: 0.6915 (t0) cc_final: 0.6699 (t0) REVERT: E 513 MET cc_start: 0.7924 (mmt) cc_final: 0.7154 (mmt) REVERT: E 698 LYS cc_start: 0.7465 (mttp) cc_final: 0.6889 (mtpt) REVERT: E 739 MET cc_start: 0.6516 (ttp) cc_final: 0.6079 (ttp) REVERT: E 790 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6872 (mtt-85) REVERT: E 819 GLU cc_start: 0.6355 (mm-30) cc_final: 0.6035 (mt-10) REVERT: E 831 GLN cc_start: 0.6122 (mm-40) cc_final: 0.5913 (mm-40) REVERT: F 123 LEU cc_start: 0.2094 (tp) cc_final: 0.1824 (tt) REVERT: G 331 LYS cc_start: 0.6371 (ptmm) cc_final: 0.5935 (pttt) REVERT: G 578 ARG cc_start: 0.5097 (tpp-160) cc_final: 0.4121 (mmm160) REVERT: G 1012 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: H 113 ARG cc_start: 0.1657 (mmp-170) cc_final: 0.1406 (mmm160) outliers start: 137 outliers final: 88 residues processed: 589 average time/residue: 0.2101 time to fit residues: 203.9547 Evaluate side-chains 538 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 435 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 151 GLN 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 339 VAL 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 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 751 LEU 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 979 GLN 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 189 THR 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 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 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 968 THR 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 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 256 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 348 CYS Chi-restraints excluded: chain E residue 398 VAL 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 727 VAL Chi-restraints excluded: chain E residue 738 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 1004 LEU Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 THR 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 204 LEU 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 470 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 755 VAL Chi-restraints excluded: chain G residue 794 ILE Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1012 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 163 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 331 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 10.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 ASN C 468 HIS C 509 ASN C 884 ASN C 887 ASN E 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 ASN E 907 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 753 HIS ** G 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN ** G1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.197651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166971 restraints weight = 42811.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166457 restraints weight = 109042.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.163798 restraints weight = 64040.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.162930 restraints weight = 50187.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.163502 restraints weight = 38001.979| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 36672 Z= 0.200 Angle : 0.637 7.995 49852 Z= 0.326 Chirality : 0.044 0.198 5744 Planarity : 0.005 0.062 6296 Dihedral : 4.560 65.469 4921 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.12 % Allowed : 16.41 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4520 helix: 0.66 (0.11), residues: 1988 sheet: -0.50 (0.26), residues: 412 loop : -0.75 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 368 TYR 0.021 0.002 TYR G 996 PHE 0.024 0.002 PHE A1000 TRP 0.025 0.002 TRP C 767 HIS 0.007 0.002 HIS E 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (36656) covalent geometry : angle 0.63736 / 0.33 (49820) SS BOND : bond 0.00260 / 0.16 ( 16) SS BOND : angle 0.52369 / 0.31 ( 32) hydrogen bonds : bond 0.05093 / 3.34 ( 1566) hydrogen bonds : angle 4.70573 / 3.41 ( 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 626 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 466 time to evaluate : 1.206 Fit side-chains REVERT: A 200 ASN cc_start: 0.5677 (m110) cc_final: 0.5439 (m-40) REVERT: A 201 ARG cc_start: 0.6396 (ttm-80) cc_final: 0.6165 (ttm-80) REVERT: A 265 ASN cc_start: 0.5899 (m-40) cc_final: 0.5493 (t0) REVERT: A 373 VAL cc_start: 0.8241 (t) cc_final: 0.7938 (p) REVERT: A 420 ASP cc_start: 0.6562 (t70) cc_final: 0.6339 (t0) REVERT: A 456 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7892 (mt) REVERT: A 481 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 562 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6514 (ttmm) REVERT: A 691 MET cc_start: 0.5996 (mmm) cc_final: 0.5779 (mtp) REVERT: A 706 THR cc_start: 0.6539 (OUTLIER) cc_final: 0.6118 (p) REVERT: A 778 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 1053 MET cc_start: 0.4847 (ppp) cc_final: 0.4403 (ptm) REVERT: B 166 LEU cc_start: 0.2714 (OUTLIER) cc_final: 0.1765 (mm) REVERT: B 209 LEU cc_start: 0.3962 (OUTLIER) cc_final: 0.3613 (pp) REVERT: C 314 MET cc_start: 0.8147 (ttp) cc_final: 0.7876 (ttm) REVERT: C 536 MET cc_start: 0.7388 (tpp) cc_final: 0.7058 (ttm) REVERT: C 739 MET cc_start: 0.5767 (mtt) cc_final: 0.5448 (mtm) REVERT: C 955 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5676 (mp0) REVERT: C 976 ARG cc_start: 0.5705 (ptt180) cc_final: 0.5270 (ptt90) REVERT: C 1027 GLN cc_start: 0.5664 (OUTLIER) cc_final: 0.5342 (mm-40) REVERT: C 1030 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7546 (mtmm) REVERT: C 1043 LEU cc_start: 0.6872 (mt) cc_final: 0.6663 (mt) REVERT: E 31 VAL cc_start: 0.6385 (OUTLIER) cc_final: 0.6083 (m) REVERT: E 324 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6171 (tt0) REVERT: E 407 ASN cc_start: 0.7431 (t0) cc_final: 0.7224 (t0) REVERT: E 513 MET cc_start: 0.8052 (mmt) cc_final: 0.7165 (mmt) REVERT: E 535 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.5842 (pt0) REVERT: E 739 MET cc_start: 0.6413 (ttp) cc_final: 0.6050 (ttt) REVERT: E 745 ASN cc_start: 0.6200 (m-40) cc_final: 0.5890 (m-40) REVERT: E 790 ARG cc_start: 0.7305 (mtt-85) cc_final: 0.7088 (mtt-85) REVERT: E 819 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5949 (mt-10) REVERT: E 907 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7306 (tm130) REVERT: E 976 ARG cc_start: 0.4253 (tpt90) cc_final: 0.3790 (tpt170) REVERT: F 123 LEU cc_start: 0.2032 (tp) cc_final: 0.1654 (tt) REVERT: G 146 LYS cc_start: 0.5131 (tptt) cc_final: 0.4915 (tppt) REVERT: G 214 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8175 (mp) REVERT: G 578 ARG cc_start: 0.5018 (tpp-160) cc_final: 0.4108 (mmm160) REVERT: G 687 ASP cc_start: 0.4904 (OUTLIER) cc_final: 0.4656 (p0) REVERT: G 1012 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: G 1051 CYS cc_start: 0.6009 (m) cc_final: 0.5541 (m) REVERT: H 113 ARG cc_start: 0.1773 (mmp-170) cc_final: 0.1509 (mmm160) outliers start: 160 outliers final: 106 residues processed: 585 average time/residue: 0.2170 time to fit residues: 208.0793 Evaluate side-chains 552 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 431 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 398 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 745 ASN 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 939 THR 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 150 LEU Chi-restraints excluded: chain C residue 189 THR 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 361 LYS Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 498 CYS 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 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 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 200 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 348 CYS Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 535 GLU 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 738 VAL Chi-restraints excluded: chain E residue 819 GLU Chi-restraints excluded: chain E residue 874 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 F residue 69 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain G residue 21 MET 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 202 SER Chi-restraints excluded: chain G residue 204 LEU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 398 VAL 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 687 ASP 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 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1012 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 329 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 204 optimal weight: 30.0000 chunk 347 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 ASN C 468 HIS E 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.199392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.168910 restraints weight = 42804.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.168270 restraints weight = 109776.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.165313 restraints weight = 65200.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.163637 restraints weight = 59894.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.164027 restraints weight = 56613.061| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36672 Z= 0.129 Angle : 0.547 10.990 49852 Z= 0.278 Chirality : 0.040 0.167 5744 Planarity : 0.005 0.080 6296 Dihedral : 4.285 65.462 4921 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 3.37 % Allowed : 17.36 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4520 helix: 0.93 (0.12), residues: 1960 sheet: -0.45 (0.26), residues: 412 loop : -0.67 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 742 TYR 0.016 0.001 TYR G 996 PHE 0.019 0.001 PHE A1000 TRP 0.032 0.001 TRP C 767 HIS 0.004 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (36656) covalent geometry : angle 0.54704 / 0.28 (49820) SS BOND : bond 0.00182 / 0.12 ( 16) SS BOND : angle 0.44516 / 0.26 ( 32) hydrogen bonds : bond 0.04309 / 2.82 ( 1566) hydrogen bonds : angle 4.52691 / 3.27 ( 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 573 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 442 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.5725 (m110) cc_final: 0.5484 (m-40) REVERT: A 201 ARG cc_start: 0.6352 (ttm-80) cc_final: 0.6037 (ttm-80) REVERT: A 265 ASN cc_start: 0.5849 (m-40) cc_final: 0.5532 (t0) REVERT: A 373 VAL cc_start: 0.8255 (t) cc_final: 0.7896 (p) REVERT: A 420 ASP cc_start: 0.6539 (t70) cc_final: 0.6247 (t0) REVERT: A 456 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8057 (mt) REVERT: A 481 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7292 (t70) REVERT: A 562 LYS cc_start: 0.6749 (mmtm) cc_final: 0.6485 (ttmm) REVERT: A 689 THR cc_start: 0.6753 (m) cc_final: 0.6387 (p) REVERT: A 691 MET cc_start: 0.6060 (mmm) cc_final: 0.5799 (mtp) REVERT: A 706 THR cc_start: 0.6501 (OUTLIER) cc_final: 0.6096 (p) REVERT: A 778 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 1053 MET cc_start: 0.4907 (ppp) cc_final: 0.4406 (ptm) REVERT: B 166 LEU cc_start: 0.2951 (OUTLIER) cc_final: 0.2044 (mm) REVERT: B 209 LEU cc_start: 0.4083 (OUTLIER) cc_final: 0.3616 (pp) REVERT: C 314 MET cc_start: 0.8055 (ttp) cc_final: 0.7808 (ttm) REVERT: C 460 MET cc_start: 0.7419 (mmt) cc_final: 0.7104 (mmt) REVERT: C 949 LEU cc_start: 0.7683 (tt) cc_final: 0.7284 (tt) REVERT: C 955 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5996 (mp0) REVERT: C 976 ARG cc_start: 0.5682 (ptt180) cc_final: 0.4778 (ptt90) REVERT: C 990 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.1980 (mt) REVERT: C 1015 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.5941 (t80) REVERT: C 1027 GLN cc_start: 0.5695 (OUTLIER) cc_final: 0.5317 (mm-40) REVERT: D 74 ARG cc_start: 0.4135 (mmt90) cc_final: 0.2309 (ttt180) REVERT: D 297 LEU cc_start: 0.5733 (OUTLIER) cc_final: 0.5428 (pp) REVERT: E 31 VAL cc_start: 0.6372 (p) cc_final: 0.6137 (m) REVERT: E 201 ARG cc_start: 0.7115 (ttm110) cc_final: 0.6728 (ttm-80) REVERT: E 513 MET cc_start: 0.8051 (mmt) cc_final: 0.7278 (mmt) REVERT: E 698 LYS cc_start: 0.7592 (mttp) cc_final: 0.7046 (mtpt) REVERT: E 739 MET cc_start: 0.6471 (ttp) cc_final: 0.6092 (ttt) REVERT: E 819 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: E 907 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: E 976 ARG cc_start: 0.4215 (tpt90) cc_final: 0.3811 (tpt170) REVERT: F 123 LEU cc_start: 0.2126 (tp) cc_final: 0.1748 (tt) REVERT: G 578 ARG cc_start: 0.4987 (tpp-160) cc_final: 0.3814 (mtm180) REVERT: G 1051 CYS cc_start: 0.6249 (m) cc_final: 0.5856 (m) outliers start: 131 outliers final: 90 residues processed: 539 average time/residue: 0.2204 time to fit residues: 195.5741 Evaluate side-chains 512 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 410 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 230 SER Chi-restraints excluded: chain A residue 261 ASP 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 523 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU 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 939 THR 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 1049 ILE Chi-restraints excluded: chain B residue 112 VAL 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 256 VAL 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 441 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR 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 933 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1004 LEU 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 D residue 97 LEU Chi-restraints excluded: chain D residue 297 LEU 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 335 SER Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 535 GLU 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 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 1005 LYS Chi-restraints excluded: chain E residue 1014 ILE Chi-restraints excluded: chain E residue 1033 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE 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 727 VAL Chi-restraints excluded: chain G residue 729 SER 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 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 171 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 124 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 407 optimal weight: 0.4980 chunk 75 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 ASN C 468 HIS E 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN H 147 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.198714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.168140 restraints weight = 42889.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168110 restraints weight = 107787.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.165806 restraints weight = 62891.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.164787 restraints weight = 51176.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165307 restraints weight = 38573.284| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36672 Z= 0.133 Angle : 0.551 9.627 49852 Z= 0.279 Chirality : 0.040 0.186 5744 Planarity : 0.005 0.068 6296 Dihedral : 4.237 65.980 4921 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 3.76 % Allowed : 17.54 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4520 helix: 0.97 (0.12), residues: 1960 sheet: -0.57 (0.26), residues: 432 loop : -0.63 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 113 TYR 0.016 0.001 TYR G 996 PHE 0.018 0.001 PHE A1000 TRP 0.029 0.001 TRP C 767 HIS 0.005 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (36656) covalent geometry : angle 0.55087 / 0.28 (49820) SS BOND : bond 0.00194 / 0.12 ( 16) SS BOND : angle 0.43692 / 0.27 ( 32) hydrogen bonds : bond 0.04310 / 2.82 ( 1566) hydrogen bonds : angle 4.50576 / 3.25 ( 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 568 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 422 time to evaluate : 1.300 Fit side-chains REVERT: A 200 ASN cc_start: 0.5707 (m110) cc_final: 0.5403 (m-40) REVERT: A 265 ASN cc_start: 0.5854 (m-40) cc_final: 0.5539 (t0) REVERT: A 373 VAL cc_start: 0.8258 (t) cc_final: 0.7868 (p) REVERT: A 374 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: A 420 ASP cc_start: 0.6569 (t70) cc_final: 0.6284 (t0) REVERT: A 456 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 481 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7329 (t70) REVERT: A 562 LYS cc_start: 0.6695 (mmtm) cc_final: 0.6292 (ttmm) REVERT: A 689 THR cc_start: 0.6624 (m) cc_final: 0.6322 (p) REVERT: A 706 THR cc_start: 0.6488 (OUTLIER) cc_final: 0.6077 (p) REVERT: A 778 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7436 (mp) REVERT: A 1053 MET cc_start: 0.4756 (ppp) cc_final: 0.4291 (ptm) REVERT: B 166 LEU cc_start: 0.2967 (OUTLIER) cc_final: 0.2016 (mm) REVERT: B 182 LEU cc_start: 0.3821 (mt) cc_final: 0.2970 (tp) REVERT: B 209 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3760 (pp) REVERT: C 314 MET cc_start: 0.8048 (ttp) cc_final: 0.7800 (ttm) REVERT: C 949 LEU cc_start: 0.7734 (tt) cc_final: 0.7382 (tt) REVERT: C 955 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6115 (mp0) REVERT: C 990 LEU cc_start: 0.2708 (OUTLIER) cc_final: 0.2053 (mt) REVERT: C 1015 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6133 (t80) REVERT: C 1027 GLN cc_start: 0.5494 (OUTLIER) cc_final: 0.5157 (mm-40) REVERT: D 74 ARG cc_start: 0.4254 (mmt90) cc_final: 0.2482 (ttt180) REVERT: D 148 LEU cc_start: 0.4682 (tp) cc_final: 0.4467 (tp) REVERT: D 297 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5345 (pp) REVERT: E 31 VAL cc_start: 0.6380 (p) cc_final: 0.6127 (m) REVERT: E 201 ARG cc_start: 0.7057 (ttm110) cc_final: 0.6716 (ttm-80) REVERT: E 442 MET cc_start: 0.7257 (mmt) cc_final: 0.7016 (tpp) REVERT: E 513 MET cc_start: 0.8012 (mmt) cc_final: 0.7295 (mmt) REVERT: E 529 LEU cc_start: 0.8152 (mp) cc_final: 0.7877 (mp) REVERT: E 698 LYS cc_start: 0.7585 (mttp) cc_final: 0.7047 (mtpt) REVERT: E 739 MET cc_start: 0.6454 (ttp) cc_final: 0.6049 (ttt) REVERT: E 819 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5647 (mt-10) REVERT: E 905 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7598 (tt) REVERT: E 907 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.6895 (tm130) REVERT: F 123 LEU cc_start: 0.2099 (tp) cc_final: 0.1742 (tt) REVERT: G 578 ARG cc_start: 0.4938 (tpp-160) cc_final: 0.3769 (mtm180) outliers start: 146 outliers final: 111 residues processed: 534 average time/residue: 0.2271 time to fit residues: 199.3362 Evaluate side-chains 526 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 401 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 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 337 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU 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 939 THR 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 112 VAL 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 256 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 689 THR Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 813 THR Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1004 LEU 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 97 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 348 CYS Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 535 GLU 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 738 VAL Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 819 GLU Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 905 LEU 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 1033 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE 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 727 VAL Chi-restraints excluded: chain G residue 729 SER 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 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 187 LEU Chi-restraints excluded: chain H residue 243 THR Chi-restraints excluded: chain H residue 246 SER Chi-restraints excluded: chain H residue 281 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: 10.0000 chunk 375 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 406 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 327 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 92 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 HIS A 884 ASN C 468 HIS C 749 HIS E 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 496 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 = 0.4119 r_free = 0.4119 target = 0.198891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.168714 restraints weight = 42787.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.168478 restraints weight = 106240.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.165357 restraints weight = 64211.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.164330 restraints weight = 54143.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165014 restraints weight = 39151.661| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36672 Z= 0.129 Angle : 0.548 9.236 49852 Z= 0.277 Chirality : 0.040 0.206 5744 Planarity : 0.004 0.061 6296 Dihedral : 4.203 66.340 4921 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.83 % Allowed : 17.57 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4520 helix: 1.01 (0.12), residues: 1960 sheet: -0.59 (0.26), residues: 432 loop : -0.64 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 790 TYR 0.021 0.001 TYR G 996 PHE 0.017 0.001 PHE A1000 TRP 0.034 0.001 TRP C 767 HIS 0.012 0.001 HIS C 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (36656) covalent geometry : angle 0.54765 / 0.28 (49820) SS BOND : bond 0.00180 / 0.11 ( 16) SS BOND : angle 0.44278 / 0.27 ( 32) hydrogen bonds : bond 0.04227 / 2.76 ( 1566) hydrogen bonds : angle 4.47996 / 3.23 ( 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 569 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 420 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 200 ASN cc_start: 0.5710 (m110) cc_final: 0.5408 (m-40) REVERT: A 265 ASN cc_start: 0.5863 (m-40) cc_final: 0.5553 (t0) REVERT: A 352 THR cc_start: 0.7934 (m) cc_final: 0.7603 (t) REVERT: A 373 VAL cc_start: 0.8273 (t) cc_final: 0.7893 (p) REVERT: A 420 ASP cc_start: 0.6604 (t70) cc_final: 0.6296 (t0) REVERT: A 453 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6738 (ttmt) REVERT: A 456 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.7999 (mt) REVERT: A 481 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7408 (t70) REVERT: A 562 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6371 (ttmm) REVERT: A 691 MET cc_start: 0.6066 (mmm) cc_final: 0.5629 (mtp) REVERT: A 706 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6089 (p) REVERT: A 778 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7444 (mp) REVERT: A 799 MET cc_start: 0.7947 (tpp) cc_final: 0.7578 (tpp) REVERT: A 996 TYR cc_start: 0.4094 (t80) cc_final: 0.3689 (t80) REVERT: A 1053 MET cc_start: 0.4696 (ppp) cc_final: 0.4283 (ptm) REVERT: B 166 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.2006 (mm) REVERT: B 182 LEU cc_start: 0.3904 (mt) cc_final: 0.3029 (tp) REVERT: B 209 LEU cc_start: 0.4209 (OUTLIER) cc_final: 0.3744 (pp) REVERT: C 314 MET cc_start: 0.8020 (ttp) cc_final: 0.7781 (ttm) REVERT: C 949 LEU cc_start: 0.7851 (tt) cc_final: 0.7513 (tt) REVERT: C 990 LEU cc_start: 0.2627 (OUTLIER) cc_final: 0.1963 (mt) REVERT: C 1015 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6110 (t80) REVERT: C 1027 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.5123 (mm-40) REVERT: D 74 ARG cc_start: 0.4248 (mmt90) cc_final: 0.2478 (ttt180) REVERT: D 297 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5296 (pp) REVERT: E 31 VAL cc_start: 0.6386 (p) cc_final: 0.6120 (m) REVERT: E 201 ARG cc_start: 0.7025 (ttm110) cc_final: 0.6704 (ttm-80) REVERT: E 343 LYS cc_start: 0.7186 (tttm) cc_final: 0.6910 (tttp) REVERT: E 513 MET cc_start: 0.8030 (mmt) cc_final: 0.7308 (mmt) REVERT: E 698 LYS cc_start: 0.7574 (mttp) cc_final: 0.7041 (mtpt) REVERT: E 905 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7571 (tt) REVERT: E 907 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7060 (tm130) REVERT: F 123 LEU cc_start: 0.1855 (tp) cc_final: 0.1542 (tt) REVERT: G 214 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8248 (mp) REVERT: G 578 ARG cc_start: 0.5051 (tpp-160) cc_final: 0.3917 (mtm180) outliers start: 149 outliers final: 118 residues processed: 529 average time/residue: 0.2047 time to fit residues: 178.9935 Evaluate side-chains 542 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 410 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 230 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 939 THR 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 112 VAL 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 256 VAL 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 361 LYS Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 523 THR 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 813 THR 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 917 VAL Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 990 LEU 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 97 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 111 THR 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 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 348 CYS Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 535 GLU 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 738 VAL Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 905 LEU 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 1033 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE 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 727 VAL Chi-restraints excluded: chain G residue 729 SER 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 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 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 281 LEU 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: 7.9990 chunk 401 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 436 optimal weight: 4.9990 chunk 419 optimal weight: 0.6980 chunk 374 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 428 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 ASN C 468 HIS C 749 HIS C1054 GLN E 468 HIS E 496 GLN ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.198450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.164881 restraints weight = 42577.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164425 restraints weight = 108702.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164682 restraints weight = 79621.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.163966 restraints weight = 49272.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.164591 restraints weight = 43685.356| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36672 Z= 0.134 Angle : 0.550 8.969 49852 Z= 0.278 Chirality : 0.040 0.193 5744 Planarity : 0.004 0.060 6296 Dihedral : 4.200 66.798 4921 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 3.94 % Allowed : 17.80 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4520 helix: 1.02 (0.12), residues: 1960 sheet: -0.60 (0.26), residues: 432 loop : -0.65 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 790 TYR 0.017 0.001 TYR G 996 PHE 0.017 0.001 PHE A1000 TRP 0.039 0.001 TRP C 767 HIS 0.013 0.001 HIS C 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (36656) covalent geometry : angle 0.55041 / 0.28 (49820) SS BOND : bond 0.00188 / 0.12 ( 16) SS BOND : angle 0.45604 / 0.27 ( 32) hydrogen bonds : bond 0.04248 / 2.78 ( 1566) hydrogen bonds : angle 4.47888 / 3.23 ( 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 572 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 419 time to evaluate : 1.044 Fit side-chains REVERT: A 200 ASN cc_start: 0.5768 (m110) cc_final: 0.5468 (m-40) REVERT: A 265 ASN cc_start: 0.5869 (m-40) cc_final: 0.5564 (t0) REVERT: A 352 THR cc_start: 0.8005 (m) cc_final: 0.7689 (t) REVERT: A 373 VAL cc_start: 0.8212 (t) cc_final: 0.7875 (p) REVERT: A 374 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: A 420 ASP cc_start: 0.6733 (t70) cc_final: 0.6404 (t0) REVERT: A 453 LYS cc_start: 0.6913 (ttpt) cc_final: 0.6695 (ttmt) REVERT: A 456 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8027 (mt) REVERT: A 481 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7403 (t70) REVERT: A 497 SER cc_start: 0.7555 (m) cc_final: 0.7247 (t) REVERT: A 562 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6304 (ttmm) REVERT: A 691 MET cc_start: 0.6134 (mmm) cc_final: 0.5841 (mtp) REVERT: A 706 THR cc_start: 0.6531 (OUTLIER) cc_final: 0.6115 (p) REVERT: A 778 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7451 (mp) REVERT: A 799 MET cc_start: 0.7894 (tpp) cc_final: 0.7557 (tpp) REVERT: A 1053 MET cc_start: 0.4682 (ppp) cc_final: 0.4336 (ptm) REVERT: B 166 LEU cc_start: 0.2969 (OUTLIER) cc_final: 0.1992 (mm) REVERT: B 182 LEU cc_start: 0.4101 (mt) cc_final: 0.3230 (tt) REVERT: B 209 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3765 (pp) REVERT: C 314 MET cc_start: 0.7999 (ttp) cc_final: 0.7761 (ttm) REVERT: C 565 MET cc_start: 0.6263 (ttm) cc_final: 0.5702 (ttt) REVERT: C 712 MET cc_start: 0.5046 (ppp) cc_final: 0.3176 (mtm) REVERT: C 749 HIS cc_start: 0.5708 (p90) cc_final: 0.5493 (p-80) REVERT: C 949 LEU cc_start: 0.7841 (tt) cc_final: 0.7542 (tt) REVERT: C 990 LEU cc_start: 0.2557 (OUTLIER) cc_final: 0.1840 (mt) REVERT: C 1015 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6132 (t80) REVERT: C 1027 GLN cc_start: 0.5439 (OUTLIER) cc_final: 0.5091 (mm-40) REVERT: D 74 ARG cc_start: 0.4379 (mmt90) cc_final: 0.2729 (ttt180) REVERT: D 277 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7442 (mp) REVERT: D 297 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5285 (pp) REVERT: E 31 VAL cc_start: 0.6330 (p) cc_final: 0.6040 (m) REVERT: E 145 TYR cc_start: 0.4783 (p90) cc_final: 0.4128 (p90) REVERT: E 201 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6676 (ttm-80) REVERT: E 343 LYS cc_start: 0.7213 (tttm) cc_final: 0.6934 (tttp) REVERT: E 513 MET cc_start: 0.8113 (mmt) cc_final: 0.7363 (mmt) REVERT: E 698 LYS cc_start: 0.7489 (mttp) cc_final: 0.7008 (mtpt) REVERT: E 905 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7463 (tt) REVERT: E 907 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6758 (tm130) REVERT: F 123 LEU cc_start: 0.1902 (tp) cc_final: 0.1580 (tt) REVERT: G 214 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8246 (mp) REVERT: G 578 ARG cc_start: 0.5052 (tpp-160) cc_final: 0.3920 (mtm180) REVERT: H 246 SER cc_start: 0.3120 (OUTLIER) cc_final: 0.2462 (p) outliers start: 153 outliers final: 120 residues processed: 538 average time/residue: 0.2142 time to fit residues: 190.3614 Evaluate side-chains 542 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 405 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 230 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 374 GLU 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 523 THR Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 939 THR 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 112 VAL 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 256 VAL 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 361 LYS Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 523 THR 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 813 THR 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 917 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 990 LEU 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 97 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 348 CYS Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 477 TRP Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 535 GLU Chi-restraints excluded: chain E residue 562 LYS 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 738 VAL Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 883 VAL Chi-restraints excluded: chain E residue 905 LEU 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 1033 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 486 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 720 VAL Chi-restraints excluded: chain G residue 727 VAL Chi-restraints excluded: chain G residue 729 SER 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 940 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 187 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 281 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: 0.9990 chunk 382 optimal weight: 0.8980 chunk 285 optimal weight: 0.0050 chunk 263 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 177 optimal weight: 0.0020 chunk 106 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 chunk 425 optimal weight: 0.3980 chunk 395 optimal weight: 0.7980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 ASN C 468 HIS E 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 826 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.200888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169672 restraints weight = 42698.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.170535 restraints weight = 101839.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.169868 restraints weight = 68332.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.169743 restraints weight = 47300.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.170372 restraints weight = 37520.916| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 36672 Z= 0.098 Angle : 0.506 8.842 49852 Z= 0.255 Chirality : 0.039 0.168 5744 Planarity : 0.004 0.055 6296 Dihedral : 3.965 67.920 4921 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.29 % Allowed : 19.42 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.13), residues: 4520 helix: 1.23 (0.12), residues: 1960 sheet: -0.53 (0.26), residues: 432 loop : -0.58 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 113 TYR 0.012 0.001 TYR G 996 PHE 0.016 0.001 PHE E 120 TRP 0.043 0.001 TRP C 767 HIS 0.003 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (36656) covalent geometry : angle 0.50569 / 0.25 (49820) SS BOND : bond 0.00133 / 0.08 ( 16) SS BOND : angle 0.40132 / 0.24 ( 32) hydrogen bonds : bond 0.03642 / 2.38 ( 1566) hydrogen bonds : angle 4.31834 / 3.10 ( 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 532 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 443 time to evaluate : 1.097 Fit side-chains REVERT: A 120 PHE cc_start: 0.7774 (t80) cc_final: 0.7545 (t80) REVERT: A 352 THR cc_start: 0.7632 (m) cc_final: 0.7400 (t) REVERT: A 420 ASP cc_start: 0.6674 (t70) cc_final: 0.6349 (t0) REVERT: A 456 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7769 (mt) REVERT: A 481 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7131 (t0) REVERT: A 562 LYS cc_start: 0.6711 (mmtm) cc_final: 0.6419 (tptm) REVERT: A 691 MET cc_start: 0.6126 (mmm) cc_final: 0.5833 (mtp) REVERT: A 706 THR cc_start: 0.6256 (OUTLIER) cc_final: 0.5903 (p) REVERT: A 745 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.4479 (t0) REVERT: A 764 LYS cc_start: 0.6055 (ttpt) cc_final: 0.4873 (mmtt) REVERT: A 799 MET cc_start: 0.7797 (tpp) cc_final: 0.7374 (tpp) REVERT: A 996 TYR cc_start: 0.3990 (t80) cc_final: 0.3579 (t80) REVERT: A 1053 MET cc_start: 0.4666 (ppp) cc_final: 0.4118 (ptm) REVERT: B 166 LEU cc_start: 0.2698 (OUTLIER) cc_final: 0.1809 (mt) REVERT: B 182 LEU cc_start: 0.4145 (mt) cc_final: 0.3266 (tt) REVERT: C 692 PHE cc_start: 0.5529 (m-10) cc_final: 0.5306 (m-10) REVERT: C 712 MET cc_start: 0.4798 (ppp) cc_final: 0.3038 (mtm) REVERT: C 767 TRP cc_start: 0.5083 (t-100) cc_final: 0.4874 (t-100) REVERT: C 949 LEU cc_start: 0.7829 (tt) cc_final: 0.7606 (tt) REVERT: C 976 ARG cc_start: 0.5711 (ptt-90) cc_final: 0.5079 (ptt-90) REVERT: C 990 LEU cc_start: 0.2250 (OUTLIER) cc_final: 0.1606 (mt) REVERT: C 1015 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6171 (t80) REVERT: C 1027 GLN cc_start: 0.5191 (OUTLIER) cc_final: 0.4982 (mm-40) REVERT: D 74 ARG cc_start: 0.4484 (mmt90) cc_final: 0.2659 (ttt180) REVERT: D 277 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7401 (mp) REVERT: D 291 ARG cc_start: 0.5781 (mmt180) cc_final: 0.5302 (mmt180) REVERT: E 23 TRP cc_start: 0.6672 (p90) cc_final: 0.6265 (p-90) REVERT: E 145 TYR cc_start: 0.4697 (p90) cc_final: 0.4146 (p90) REVERT: E 201 ARG cc_start: 0.6897 (ttm110) cc_final: 0.6569 (ttm-80) REVERT: E 266 PHE cc_start: 0.7208 (m-10) cc_final: 0.6900 (m-80) REVERT: E 343 LYS cc_start: 0.7124 (tttm) cc_final: 0.6896 (tttp) REVERT: E 513 MET cc_start: 0.8009 (mmt) cc_final: 0.7152 (mmt) REVERT: E 698 LYS cc_start: 0.7428 (mttp) cc_final: 0.6957 (mtpt) REVERT: E 977 VAL cc_start: 0.6529 (m) cc_final: 0.6162 (t) REVERT: F 123 LEU cc_start: 0.2310 (tp) cc_final: 0.1823 (tt) REVERT: G 214 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8283 (mp) REVERT: G 228 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6807 (mtpp) REVERT: G 578 ARG cc_start: 0.4960 (tpp-160) cc_final: 0.3719 (mtp85) REVERT: H 246 SER cc_start: 0.2960 (OUTLIER) cc_final: 0.2312 (p) outliers start: 89 outliers final: 57 residues processed: 509 average time/residue: 0.2068 time to fit residues: 173.3998 Evaluate side-chains 486 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 418 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 308 ILE 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 745 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 968 THR 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 166 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 324 GLU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 689 THR 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 917 VAL Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 946 THR Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 990 LEU Chi-restraints excluded: chain C residue 1015 TYR Chi-restraints excluded: chain C residue 1027 GLN Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 720 VAL Chi-restraints excluded: chain E residue 727 VAL Chi-restraints excluded: chain E residue 745 ASN 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 F residue 287 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 398 VAL Chi-restraints excluded: chain G residue 470 LEU Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 581 ILE Chi-restraints excluded: chain G residue 729 SER Chi-restraints excluded: chain G residue 826 ASN Chi-restraints excluded: chain G residue 886 THR Chi-restraints excluded: chain G residue 940 LEU Chi-restraints excluded: chain G residue 949 LEU 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 281 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: 6.9990 chunk 149 optimal weight: 8.9990 chunk 444 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 331 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 884 ASN C 468 HIS ** E 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 907 GLN G 449 ASN G 496 GLN ** G 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 806 ASN G 826 ASN G 907 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.197641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.166009 restraints weight = 42485.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.166609 restraints weight = 101607.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164609 restraints weight = 67116.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.164122 restraints weight = 46920.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.164457 restraints weight = 38869.764| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36672 Z= 0.148 Angle : 0.573 13.369 49852 Z= 0.287 Chirality : 0.041 0.200 5744 Planarity : 0.005 0.058 6296 Dihedral : 4.087 69.899 4920 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 2.31 % Allowed : 19.37 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.12), residues: 4520 helix: 1.12 (0.12), residues: 1952 sheet: -0.57 (0.26), residues: 432 loop : -0.65 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 113 TYR 0.019 0.002 TYR G 996 PHE 0.018 0.002 PHE A1000 TRP 0.035 0.002 TRP C 767 HIS 0.006 0.001 HIS A 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (36656) covalent geometry : angle 0.57302 / 0.29 (49820) SS BOND : bond 0.00188 / 0.11 ( 16) SS BOND : angle 0.48897 / 0.28 ( 32) hydrogen bonds : bond 0.04295 / 2.81 ( 1566) hydrogen bonds : angle 4.43359 / 3.20 ( 4392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5959.70 seconds wall clock time: 103 minutes 52.76 seconds (6232.76 seconds total)