Starting phenix.real_space_refine on Tue Aug 26 10:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.map" model { file = "/net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yo0_33977/08_2025/7yo0_33977.cif" } resolution = 3.6 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= 0.004 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 Mg 4 5.21 5 S 228 5.16 5 C 23276 2.51 5 N 6040 2.21 5 O 6444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36004 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: {'PCIS': 1, 'PTRANS': 21, '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: {'PCIS': 1, 'PTRANS': 21, '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: {'PCIS': 1, 'PTRANS': 21, '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: {'PCIS': 1, 'PTRANS': 21, '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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 2, ' MG': 1, 'PGW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 2, ' MG': 1, 'PGW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 2, ' MG': 1, 'PGW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 2, ' MG': 1, 'PGW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.37, per 1000 atoms: 0.20 Number of scatterers: 36004 At special positions: 0 Unit cell: (162.348, 162.348, 175.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 S 228 16.00 P 4 15.00 Mg 4 11.99 O 6444 8.00 N 6040 7.00 C 23276 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=2.03 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=2.03 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8600 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 28 sheets defined 48.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.505A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (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 143 through 147 removed outlier: 3.570A pdb=" N ASP A 147 " --> pdb=" O PHE A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 171 removed outlier: 3.903A pdb=" N ILE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.502A pdb=" N LEU A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.408A 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: 4.114A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.075A 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 393 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.525A pdb=" N LYS A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.503A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 529 removed outlier: 4.140A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.917A pdb=" N VAL A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 555' 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 759 through 766 removed outlier: 3.564A pdb=" N LEU A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 817 through 830 removed outlier: 3.769A pdb=" N LEU A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.341A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.546A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) 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: 3.535A pdb=" N VAL A 919 " --> pdb=" O ALA A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.621A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.131A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 removed outlier: 3.503A 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 991 removed outlier: 4.425A pdb=" N ASP A 989 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.878A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.739A pdb=" N LEU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.557A 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: 4.016A 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: 3.720A 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 234 through 238 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.506A pdb=" N PHE B 245 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 297 removed outlier: 3.603A pdb=" N TYR B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.505A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.570A pdb=" N ASP C 147 " --> pdb=" O PHE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 171 removed outlier: 3.903A pdb=" N ILE C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.502A pdb=" N LEU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 205 through 215 removed outlier: 4.408A 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: 4.114A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 4.075A 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 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.525A pdb=" N LYS C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.503A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 529 removed outlier: 4.140A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 555 removed outlier: 3.917A pdb=" N VAL C 553 " --> pdb=" O SER C 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 555' 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 759 through 766 removed outlier: 3.564A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 769 No H-bonds generated for 'chain 'C' and resid 767 through 769' 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 removed outlier: 3.913A pdb=" N ILE C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU C 822 " --> pdb=" O LYS C 818 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA C 823 " --> pdb=" O GLU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.341A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.546A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 3.584A 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 921 removed outlier: 3.535A pdb=" N VAL C 919 " --> pdb=" O ALA C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 930 removed outlier: 3.621A pdb=" N ASN C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 941 removed outlier: 4.131A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 removed outlier: 3.503A pdb=" N ALA C 951 " --> pdb=" O PRO C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 971 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.425A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.878A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.739A pdb=" N LEU D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 164' Processing helix chain 'D' and resid 186 through 190 removed outlier: 4.016A 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: 3.720A pdb=" N ARG D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 241 through 245 removed outlier: 3.506A pdb=" N PHE D 245 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 297 removed outlier: 3.603A pdb=" N TYR D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.728A 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 removed outlier: 3.505A pdb=" N LEU E 26 " --> pdb=" O TRP E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 106 Processing helix chain 'E' and resid 109 through 134 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.570A pdb=" N ASP E 147 " --> pdb=" O PHE E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 171 removed outlier: 3.903A pdb=" N ILE E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 179 removed outlier: 3.502A pdb=" N LEU E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 200 Proline residue: E 191 - end of helix Processing helix chain 'E' and resid 205 through 215 removed outlier: 4.408A 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: 4.114A pdb=" N LEU E 309 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY E 310 " --> pdb=" O PHE E 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) removed outlier: 4.075A 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 393 Processing helix chain 'E' and resid 407 through 414 Processing helix chain 'E' and resid 415 through 417 No H-bonds generated for 'chain 'E' and resid 415 through 417' Processing helix chain 'E' and resid 432 through 451 Processing helix chain 'E' and resid 462 through 471 removed outlier: 3.525A pdb=" N LYS E 466 " --> pdb=" O GLN E 462 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 500 Processing helix chain 'E' and resid 502 through 510 removed outlier: 3.503A pdb=" N MET E 506 " --> pdb=" O GLY E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 529 removed outlier: 4.140A pdb=" N TYR E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 555 removed outlier: 3.917A pdb=" N VAL E 553 " --> pdb=" O SER E 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS E 554 " --> pdb=" O PHE E 550 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 549 through 555' Processing helix chain 'E' and resid 557 through 562 Processing helix chain 'E' and resid 699 through 703 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 766 removed outlier: 3.564A pdb=" N LEU E 763 " --> pdb=" O SER E 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 769 No H-bonds generated for 'chain 'E' and resid 767 through 769' Processing helix chain 'E' and resid 785 through 792 Processing helix chain 'E' and resid 806 through 809 Processing helix chain 'E' and resid 817 through 830 removed outlier: 3.808A pdb=" N LEU E 822 " --> pdb=" O LYS E 818 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA E 823 " --> pdb=" O GLU E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 876 removed outlier: 4.341A pdb=" N ASN E 875 " --> pdb=" O THR E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 884 through 891 removed outlier: 3.546A pdb=" N ASN E 887 " --> pdb=" O ASN E 884 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN E 889 " --> pdb=" O THR E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 905 Processing helix chain 'E' and resid 906 through 911 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.535A pdb=" N VAL E 919 " --> pdb=" O ALA E 916 " (cutoff:3.500A) Processing helix chain 'E' and resid 922 through 930 removed outlier: 3.621A pdb=" N ASN E 930 " --> pdb=" O ALA E 926 " (cutoff:3.500A) Processing helix chain 'E' and resid 931 through 941 removed outlier: 4.131A pdb=" N THR E 935 " --> pdb=" O ASP E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 946 through 957 removed outlier: 3.503A pdb=" N ALA E 951 " --> pdb=" O PRO E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 965 through 971 Processing helix chain 'E' and resid 985 through 991 removed outlier: 4.425A pdb=" N ASP E 989 " --> pdb=" O PRO E 986 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1008 removed outlier: 3.878A pdb=" N LEU E 999 " --> pdb=" O CYS E 995 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.739A pdb=" N LEU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 164' Processing helix chain 'F' and resid 186 through 190 removed outlier: 4.016A 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: 3.720A pdb=" N ARG F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 227 Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 241 through 245 removed outlier: 3.506A pdb=" N PHE F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 297 removed outlier: 3.603A pdb=" N TYR F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 4.728A 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 removed outlier: 3.505A pdb=" N LEU G 26 " --> pdb=" O TRP G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 Processing helix chain 'G' and resid 109 through 134 Processing helix chain 'G' and resid 143 through 147 removed outlier: 3.570A pdb=" N ASP G 147 " --> pdb=" O PHE G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 171 removed outlier: 3.903A pdb=" N ILE G 152 " --> pdb=" O PHE G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 179 removed outlier: 3.502A pdb=" N LEU G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 200 Proline residue: G 191 - end of helix Processing helix chain 'G' and resid 205 through 215 removed outlier: 4.408A 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: 4.114A pdb=" N LEU G 309 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY G 310 " --> pdb=" O PHE G 306 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA G 313 " --> pdb=" O LEU G 309 " (cutoff:3.500A) removed outlier: 4.075A 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 393 Processing helix chain 'G' and resid 407 through 414 Processing helix chain 'G' and resid 415 through 417 No H-bonds generated for 'chain 'G' and resid 415 through 417' Processing helix chain 'G' and resid 432 through 451 Processing helix chain 'G' and resid 462 through 471 removed outlier: 3.525A pdb=" N LYS G 466 " --> pdb=" O GLN G 462 " (cutoff:3.500A) removed outlier: 3.769A 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 510 removed outlier: 3.503A pdb=" N MET G 506 " --> pdb=" O GLY G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 529 removed outlier: 4.140A pdb=" N TYR G 527 " --> pdb=" O THR G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 555 removed outlier: 3.917A pdb=" N VAL G 553 " --> pdb=" O SER G 549 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS G 554 " --> pdb=" O PHE G 550 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 555 " --> pdb=" O PRO G 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 549 through 555' Processing helix chain 'G' and resid 557 through 562 Processing helix chain 'G' and resid 699 through 703 Processing helix chain 'G' and resid 706 through 713 Processing helix chain 'G' and resid 734 through 739 Processing helix chain 'G' and resid 759 through 766 removed outlier: 3.564A pdb=" N LEU G 763 " --> pdb=" O SER G 759 " (cutoff:3.500A) Processing helix chain 'G' and resid 767 through 769 No H-bonds generated for 'chain 'G' and resid 767 through 769' Processing helix chain 'G' and resid 785 through 792 Processing helix chain 'G' and resid 806 through 809 Processing helix chain 'G' and resid 817 through 830 Processing helix chain 'G' and resid 872 through 876 removed outlier: 4.341A pdb=" N ASN G 875 " --> pdb=" O THR G 872 " (cutoff:3.500A) Processing helix chain 'G' and resid 884 through 891 removed outlier: 3.546A pdb=" N ASN G 887 " --> pdb=" O ASN G 884 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN G 889 " --> pdb=" O THR G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 902 through 905 Processing helix chain 'G' and resid 906 through 911 Processing helix chain 'G' and resid 916 through 921 removed outlier: 3.535A pdb=" N VAL G 919 " --> pdb=" O ALA G 916 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 930 removed outlier: 3.621A pdb=" N ASN G 930 " --> pdb=" O ALA G 926 " (cutoff:3.500A) Processing helix chain 'G' and resid 931 through 941 removed outlier: 4.131A pdb=" N THR G 935 " --> pdb=" O ASP G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 946 through 957 removed outlier: 3.503A pdb=" N ALA G 951 " --> pdb=" O PRO G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 965 through 971 Processing helix chain 'G' and resid 985 through 991 removed outlier: 4.425A pdb=" N ASP G 989 " --> pdb=" O PRO G 986 " (cutoff:3.500A) Processing helix chain 'G' and resid 995 through 1008 removed outlier: 3.878A pdb=" N LEU G 999 " --> pdb=" O CYS G 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.739A pdb=" N LEU H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 159 through 164' Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.016A pdb=" N ARG H 189 " --> pdb=" O LEU H 186 " (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: 3.720A 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 234 through 238 Processing helix chain 'H' and resid 241 through 245 removed outlier: 3.506A pdb=" N PHE H 245 " --> pdb=" O LEU H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 297 removed outlier: 3.603A pdb=" N TYR H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 4.728A 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 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.768A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS A 344 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS A 422 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 346 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A 424 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS A 348 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE A 457 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 458 " --> pdb=" O ASP A 482 " (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: 6.072A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.247A 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: 4.132A pdb=" N PHE A1050 " --> pdb=" O GLY A1013 " (cutoff:3.500A) removed outlier: 4.931A 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: 3.721A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.912A 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: 3.942A 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 140 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 402 removed outlier: 3.768A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS C 344 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS C 422 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 346 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 424 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS C 348 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE C 457 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 458 " --> pdb=" O ASP C 482 " (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 779 removed outlier: 6.072A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.247A 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 980 removed outlier: 4.132A pdb=" N PHE C1050 " --> pdb=" O GLY C1013 " (cutoff:3.500A) removed outlier: 4.931A 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: 3.721A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.912A 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: 3.942A 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: 3.768A pdb=" N HIS E 379 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY E 349 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS E 344 " --> pdb=" O ASP E 420 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS E 422 " --> pdb=" O HIS E 344 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 346 " --> pdb=" O CYS E 422 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE E 424 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS E 348 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE E 457 " --> pdb=" O ASP E 420 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS E 422 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN E 459 " --> pdb=" O CYS E 422 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE E 424 " --> pdb=" O GLN E 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 458 " --> pdb=" O ASP E 482 " (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 779 removed outlier: 6.072A pdb=" N CYS E 800 " --> pdb=" O ILE E 879 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU E 881 " --> pdb=" O CYS E 800 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE E 802 " --> pdb=" O GLU E 881 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE E 915 " --> pdb=" O ILE E 878 " (cutoff:3.500A) removed outlier: 6.247A 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 980 removed outlier: 4.132A pdb=" N PHE E1050 " --> pdb=" O GLY E1013 " (cutoff:3.500A) removed outlier: 4.931A 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: 3.721A pdb=" N LEU F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.912A 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 removed outlier: 3.942A pdb=" N LEU F 86 " --> pdb=" O SER F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 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: 3.768A pdb=" N HIS G 379 " --> pdb=" O TYR G 401 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY G 349 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N HIS G 344 " --> pdb=" O ASP G 420 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N CYS G 422 " --> pdb=" O HIS G 344 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL G 346 " --> pdb=" O CYS G 422 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE G 424 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS G 348 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE G 457 " --> pdb=" O ASP G 420 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS G 422 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN G 459 " --> pdb=" O CYS G 422 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE G 424 " --> pdb=" O GLN G 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR G 458 " --> pdb=" O ASP G 482 " (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 779 removed outlier: 6.072A pdb=" N CYS G 800 " --> pdb=" O ILE G 879 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLU G 881 " --> pdb=" O CYS G 800 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE G 802 " --> pdb=" O GLU G 881 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE G 915 " --> pdb=" O ILE G 878 " (cutoff:3.500A) removed outlier: 6.247A 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 980 removed outlier: 4.132A pdb=" N PHE G1050 " --> pdb=" O GLY G1013 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY G1013 " --> pdb=" O PHE G1050 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 48 through 50 removed outlier: 3.721A pdb=" N LEU H 54 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.912A 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: 3.942A pdb=" N LEU H 86 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1525 hydrogen bonds defined for protein. 4179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5749 1.31 - 1.43: 9881 1.43 - 1.56: 20852 1.56 - 1.69: 10 1.69 - 1.81: 320 Bond restraints: 36812 Sorted by residual: bond pdb=" C GLU A 819 " pdb=" O GLU A 819 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.26e-02 6.30e+03 1.79e+01 bond pdb=" C GLN A 816 " pdb=" O GLN A 816 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.26e-02 6.30e+03 1.68e+01 bond pdb=" CA LYS A 818 " pdb=" C LYS A 818 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.56e+01 bond pdb=" CA LYS C 818 " pdb=" C LYS C 818 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" CA GLN A 816 " pdb=" C GLN A 816 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.34e-02 5.57e+03 1.43e+01 ... (remaining 36807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 49699 2.80 - 5.59: 280 5.59 - 8.39: 15 8.39 - 11.19: 4 11.19 - 13.98: 2 Bond angle restraints: 50000 Sorted by residual: angle pdb=" N LYS C 818 " pdb=" CA LYS C 818 " pdb=" C LYS C 818 " ideal model delta sigma weight residual 112.54 98.56 13.98 1.22e+00 6.72e-01 1.31e+02 angle pdb=" N GLU E 819 " pdb=" CA GLU E 819 " pdb=" C GLU E 819 " ideal model delta sigma weight residual 110.80 99.04 11.76 2.13e+00 2.20e-01 3.05e+01 angle pdb=" N ILE G 441 " pdb=" CA ILE G 441 " pdb=" C ILE G 441 " ideal model delta sigma weight residual 111.09 104.39 6.70 1.25e+00 6.40e-01 2.88e+01 angle pdb=" N GLN A 816 " pdb=" CA GLN A 816 " pdb=" C GLN A 816 " ideal model delta sigma weight residual 110.80 121.37 -10.57 2.13e+00 2.20e-01 2.46e+01 angle pdb=" N VAL A 444 " pdb=" CA VAL A 444 " pdb=" C VAL A 444 " ideal model delta sigma weight residual 110.23 105.18 5.05 1.04e+00 9.25e-01 2.36e+01 ... (remaining 49995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 20687 25.25 - 50.49: 1106 50.49 - 75.74: 72 75.74 - 100.98: 19 100.98 - 126.23: 28 Dihedral angle restraints: 21912 sinusoidal: 8632 harmonic: 13280 Sorted by residual: dihedral pdb=" C15 PGW G1101 " pdb=" C26 PGW G1101 " pdb=" C27 PGW G1101 " pdb=" C25 PGW G1101 " ideal model delta sinusoidal sigma weight residual -174.86 -48.63 -126.23 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C15 PGW E1101 " pdb=" C26 PGW E1101 " pdb=" C27 PGW E1101 " pdb=" C25 PGW E1101 " ideal model delta sinusoidal sigma weight residual -174.86 -48.63 -126.23 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C15 PGW A1101 " pdb=" C26 PGW A1101 " pdb=" C27 PGW A1101 " pdb=" C25 PGW A1101 " ideal model delta sinusoidal sigma weight residual -174.86 -48.63 -126.23 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 21909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3807 0.033 - 0.066: 1408 0.066 - 0.099: 377 0.099 - 0.131: 145 0.131 - 0.164: 15 Chirality restraints: 5752 Sorted by residual: chirality pdb=" CA ARG B 294 " pdb=" N ARG B 294 " pdb=" C ARG B 294 " pdb=" CB ARG B 294 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ARG D 294 " pdb=" N ARG D 294 " pdb=" C ARG D 294 " pdb=" CB ARG D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ARG H 294 " pdb=" N ARG H 294 " pdb=" C ARG H 294 " pdb=" CB ARG H 294 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 5749 not shown) Planarity restraints: 6304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 815 " -0.026 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C LEU C 815 " 0.086 2.00e-02 2.50e+03 pdb=" O LEU C 815 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN C 816 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 816 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLN G 816 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN G 816 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP G 817 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 438 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C ALA G 438 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA G 438 " 0.020 2.00e-02 2.50e+03 pdb=" N SER G 439 " 0.018 2.00e-02 2.50e+03 ... (remaining 6301 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 121 2.45 - 3.07: 23314 3.07 - 3.68: 54423 3.68 - 4.29: 78560 4.29 - 4.90: 133143 Nonbonded interactions: 289561 Sorted by model distance: nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR E 290 " model vdw 1.844 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR C 290 " model vdw 1.844 3.040 nonbonded pdb=" OG1 THR E 284 " pdb=" OH TYR G 290 " model vdw 1.844 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR G 284 " model vdw 1.844 3.040 nonbonded pdb=" ND2 ASN A 449 " pdb=" O GLN C 889 " model vdw 1.925 3.120 ... (remaining 289556 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' 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: 1.720 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 29.970 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36828 Z= 0.185 Angle : 0.545 13.982 50032 Z= 0.315 Chirality : 0.039 0.164 5752 Planarity : 0.004 0.052 6304 Dihedral : 14.843 126.226 13264 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.35 % Favored : 97.41 % Rotamer: Outliers : 1.08 % Allowed : 0.15 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.13), residues: 4520 helix: 1.13 (0.12), residues: 1848 sheet: 0.39 (0.28), residues: 412 loop : -0.43 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 293 TYR 0.011 0.001 TYR G1007 PHE 0.010 0.001 PHE G 120 TRP 0.006 0.001 TRP C 475 HIS 0.003 0.000 HIS E 464 Details of bonding type rmsd covalent geometry : bond 0.00291 (36812) covalent geometry : angle 0.54479 (50000) SS BOND : bond 0.00078 ( 16) SS BOND : angle 0.38642 ( 32) hydrogen bonds : bond 0.17950 ( 1525) hydrogen bonds : angle 6.31507 ( 4179) *********************** 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 1021 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 979 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.8114 (tt) cc_final: 0.7733 (mt) REVERT: A 42 LEU cc_start: 0.7907 (tt) cc_final: 0.7690 (tp) REVERT: A 94 MET cc_start: 0.7890 (mmm) cc_final: 0.7665 (tpp) REVERT: A 603 LYS cc_start: 0.5685 (tppt) cc_final: 0.5357 (tppt) REVERT: A 604 GLU cc_start: 0.6030 (pm20) cc_final: 0.5740 (pt0) REVERT: A 739 MET cc_start: 0.7242 (mtp) cc_final: 0.6979 (mtt) REVERT: A 764 LYS cc_start: 0.7410 (tmmt) cc_final: 0.6941 (mtpt) REVERT: A 778 ILE cc_start: 0.7591 (mp) cc_final: 0.7374 (mt) REVERT: A 782 THR cc_start: 0.8118 (t) cc_final: 0.7895 (p) REVERT: A 798 ASP cc_start: 0.6869 (t0) cc_final: 0.6497 (t0) REVERT: B 77 LEU cc_start: 0.5144 (mm) cc_final: 0.4545 (tp) REVERT: B 97 LEU cc_start: 0.5853 (tp) cc_final: 0.5576 (tt) REVERT: B 102 LEU cc_start: 0.6226 (mt) cc_final: 0.5974 (mp) REVERT: B 110 VAL cc_start: 0.6011 (t) cc_final: 0.5633 (p) REVERT: B 127 SER cc_start: 0.6899 (p) cc_final: 0.6208 (m) REVERT: B 257 LEU cc_start: 0.5418 (tp) cc_final: 0.5042 (pt) REVERT: B 259 LEU cc_start: 0.6251 (mt) cc_final: 0.6020 (mt) REVERT: B 276 SER cc_start: 0.8098 (t) cc_final: 0.7770 (p) REVERT: C 34 PHE cc_start: 0.6198 (m-10) cc_final: 0.5870 (m-80) REVERT: C 94 MET cc_start: 0.7491 (mmm) cc_final: 0.7275 (tpp) REVERT: C 133 ASP cc_start: 0.6739 (m-30) cc_final: 0.6472 (m-30) REVERT: C 268 ASN cc_start: 0.7329 (m-40) cc_final: 0.6798 (m-40) REVERT: C 282 MET cc_start: 0.8125 (tpt) cc_final: 0.7810 (tpt) REVERT: C 380 ASN cc_start: 0.8038 (m-40) cc_final: 0.7720 (m-40) REVERT: C 518 LYS cc_start: 0.5973 (ttpt) cc_final: 0.5629 (mtmt) REVERT: C 564 LEU cc_start: 0.8445 (tp) cc_final: 0.8035 (tp) REVERT: C 604 GLU cc_start: 0.7434 (pm20) cc_final: 0.6973 (pm20) REVERT: C 759 SER cc_start: 0.6023 (t) cc_final: 0.5664 (m) REVERT: C 784 LEU cc_start: 0.8371 (mt) cc_final: 0.8107 (mm) REVERT: C 825 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8092 (mp) REVERT: C 950 GLU cc_start: 0.6428 (mm-30) cc_final: 0.5876 (mt-10) REVERT: C 1022 LEU cc_start: 0.4788 (mt) cc_final: 0.4570 (mt) REVERT: E 23 TRP cc_start: 0.5703 (p90) cc_final: 0.5329 (t-100) REVERT: E 200 ASN cc_start: 0.7364 (m-40) cc_final: 0.7094 (t0) REVERT: E 216 GLN cc_start: 0.6752 (mp10) cc_final: 0.6418 (pp30) REVERT: E 340 SER cc_start: 0.7247 (p) cc_final: 0.7011 (m) REVERT: E 515 SER cc_start: 0.8034 (p) cc_final: 0.7780 (t) REVERT: E 564 LEU cc_start: 0.8027 (tp) cc_final: 0.7785 (tt) REVERT: E 802 ILE cc_start: 0.8418 (mm) cc_final: 0.8104 (mm) REVERT: E 886 THR cc_start: 0.7543 (m) cc_final: 0.7071 (p) REVERT: E 1009 MET cc_start: 0.6674 (mmt) cc_final: 0.4288 (mtt) REVERT: F 82 ARG cc_start: 0.6219 (mtt90) cc_final: 0.5370 (ttp-110) REVERT: F 148 LEU cc_start: 0.6167 (tp) cc_final: 0.5692 (pp) REVERT: F 182 LEU cc_start: 0.3966 (mt) cc_final: 0.3302 (tp) REVERT: G 404 SER cc_start: 0.7191 (t) cc_final: 0.6815 (t) REVERT: G 420 ASP cc_start: 0.7046 (t70) cc_final: 0.6672 (t0) REVERT: G 538 THR cc_start: 0.7770 (m) cc_final: 0.7554 (p) REVERT: G 732 ILE cc_start: 0.6535 (mt) cc_final: 0.6274 (mt) REVERT: G 1002 LYS cc_start: 0.7378 (tmtt) cc_final: 0.6914 (tptm) REVERT: G 1021 HIS cc_start: 0.7740 (p-80) cc_final: 0.7072 (p-80) REVERT: H 103 ARG cc_start: 0.5862 (ttm-80) cc_final: 0.5442 (mmm-85) REVERT: H 149 SER cc_start: 0.5750 (m) cc_final: 0.5159 (p) REVERT: H 210 ARG cc_start: 0.3048 (mmm160) cc_final: 0.2539 (ttp80) REVERT: H 259 LEU cc_start: 0.5777 (mt) cc_final: 0.5415 (mt) REVERT: H 266 TYR cc_start: 0.6803 (m-80) cc_final: 0.6549 (m-80) REVERT: H 294 ARG cc_start: 0.5185 (mmt180) cc_final: 0.4666 (mtm110) outliers start: 42 outliers final: 18 residues processed: 1010 average time/residue: 0.2102 time to fit residues: 336.6237 Evaluate side-chains 572 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 553 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 825 LEU Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 818 LYS Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 825 LEU Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 441 ILE Chi-restraints excluded: chain G residue 818 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.0050 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 0.1980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 397 GLN A 887 ASN A1021 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 222 GLN C 402 GLN C 884 ASN E 222 GLN E 372 ASN E 887 ASN E 889 GLN F 108 HIS G 222 GLN G 831 GLN G 887 ASN H 201 ASN H 252 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.191798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.157668 restraints weight = 50566.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155334 restraints weight = 78179.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157041 restraints weight = 70394.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157064 restraints weight = 46826.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158516 restraints weight = 40489.541| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36828 Z= 0.127 Angle : 0.567 10.285 50032 Z= 0.285 Chirality : 0.041 0.185 5752 Planarity : 0.004 0.049 6304 Dihedral : 9.275 117.690 5109 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.88 % Allowed : 10.21 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.13), residues: 4520 helix: 1.03 (0.12), residues: 1944 sheet: 0.31 (0.28), residues: 436 loop : -0.39 (0.14), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 199 TYR 0.018 0.001 TYR C 928 PHE 0.018 0.001 PHE G1000 TRP 0.017 0.001 TRP A 477 HIS 0.007 0.001 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00281 (36812) covalent geometry : angle 0.56640 (50000) SS BOND : bond 0.00664 ( 16) SS BOND : angle 0.91079 ( 32) hydrogen bonds : bond 0.04107 ( 1525) hydrogen bonds : angle 4.92146 ( 4179) *********************** 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 660 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 587 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8105 (tt) cc_final: 0.7861 (tp) REVERT: A 511 PHE cc_start: 0.7444 (m-10) cc_final: 0.7135 (m-10) REVERT: A 513 MET cc_start: 0.8505 (mmm) cc_final: 0.7608 (mmt) REVERT: A 603 LYS cc_start: 0.5758 (tppt) cc_final: 0.5549 (tppt) REVERT: A 604 GLU cc_start: 0.6115 (pm20) cc_final: 0.5316 (pt0) REVERT: A 798 ASP cc_start: 0.6635 (t0) cc_final: 0.6237 (t0) REVERT: A 900 ASP cc_start: 0.6844 (m-30) cc_final: 0.6595 (m-30) REVERT: A 1009 MET cc_start: 0.5050 (mmp) cc_final: 0.4305 (mmm) REVERT: B 71 LEU cc_start: 0.4969 (tp) cc_final: 0.4691 (tp) REVERT: B 77 LEU cc_start: 0.5266 (mm) cc_final: 0.4852 (tp) REVERT: B 110 VAL cc_start: 0.5653 (t) cc_final: 0.5373 (p) REVERT: C 34 PHE cc_start: 0.6312 (m-10) cc_final: 0.5949 (m-80) REVERT: C 264 GLU cc_start: 0.7036 (tt0) cc_final: 0.6752 (tt0) REVERT: C 282 MET cc_start: 0.8184 (tpt) cc_final: 0.7847 (tpt) REVERT: C 314 MET cc_start: 0.8130 (tmm) cc_final: 0.7416 (tmm) REVERT: C 337 SER cc_start: 0.8647 (t) cc_final: 0.8357 (p) REVERT: C 380 ASN cc_start: 0.8148 (m-40) cc_final: 0.7896 (m-40) REVERT: C 950 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5755 (mt-10) REVERT: D 116 TRP cc_start: 0.3426 (OUTLIER) cc_final: 0.2429 (m100) REVERT: E 23 TRP cc_start: 0.5730 (p90) cc_final: 0.5476 (t-100) REVERT: E 216 GLN cc_start: 0.7021 (mp10) cc_final: 0.6674 (pp30) REVERT: E 306 PHE cc_start: 0.7718 (m-80) cc_final: 0.7478 (m-10) REVERT: E 340 SER cc_start: 0.7358 (p) cc_final: 0.7157 (m) REVERT: E 1009 MET cc_start: 0.6456 (mmt) cc_final: 0.4309 (mtt) REVERT: F 82 ARG cc_start: 0.5617 (mtt90) cc_final: 0.5310 (ttp-110) REVERT: F 148 LEU cc_start: 0.6196 (tp) cc_final: 0.5797 (pp) REVERT: F 182 LEU cc_start: 0.3666 (mt) cc_final: 0.3028 (tp) REVERT: G 449 ASN cc_start: 0.6254 (t0) cc_final: 0.6013 (t0) REVERT: G 538 THR cc_start: 0.7864 (m) cc_final: 0.7558 (p) REVERT: G 732 ILE cc_start: 0.6753 (mt) cc_final: 0.6515 (mt) REVERT: G 1002 LYS cc_start: 0.7221 (tmtt) cc_final: 0.6951 (tptm) REVERT: G 1009 MET cc_start: 0.4530 (mmt) cc_final: 0.4280 (mmm) REVERT: G 1021 HIS cc_start: 0.7608 (p-80) cc_final: 0.7072 (p-80) REVERT: H 116 TRP cc_start: 0.2419 (OUTLIER) cc_final: 0.1566 (m100) REVERT: H 294 ARG cc_start: 0.5543 (mmt180) cc_final: 0.4867 (mtm110) outliers start: 73 outliers final: 45 residues processed: 642 average time/residue: 0.1825 time to fit residues: 193.0897 Evaluate side-chains 513 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 466 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 887 ASN Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 439 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 874 VAL Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 930 ASN Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 818 LYS Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 880 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 128 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 143 optimal weight: 0.0040 chunk 454 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 455 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS A 427 ASN A1021 HIS B 98 GLN C 509 ASN E 496 GLN G 182 ASN G 216 GLN G 771 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.189229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153351 restraints weight = 50095.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151834 restraints weight = 76077.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153684 restraints weight = 69431.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153874 restraints weight = 44809.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155199 restraints weight = 39937.457| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36828 Z= 0.116 Angle : 0.529 9.745 50032 Z= 0.265 Chirality : 0.040 0.161 5752 Planarity : 0.004 0.049 6304 Dihedral : 8.299 119.994 5078 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.98 % Allowed : 12.45 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.13), residues: 4520 helix: 1.01 (0.12), residues: 2020 sheet: 0.06 (0.28), residues: 412 loop : -0.46 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 103 TYR 0.018 0.001 TYR E 996 PHE 0.022 0.001 PHE G1000 TRP 0.018 0.001 TRP C 477 HIS 0.006 0.001 HIS E 365 Details of bonding type rmsd covalent geometry : bond 0.00261 (36812) covalent geometry : angle 0.52890 (50000) SS BOND : bond 0.00192 ( 16) SS BOND : angle 0.62122 ( 32) hydrogen bonds : bond 0.03831 ( 1525) hydrogen bonds : angle 4.63020 ( 4179) *********************** 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 604 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 527 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5711 (tmm160) cc_final: 0.5101 (tmt170) REVERT: A 42 LEU cc_start: 0.8083 (tt) cc_final: 0.7857 (tp) REVERT: A 321 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: A 513 MET cc_start: 0.8490 (mmm) cc_final: 0.7507 (mmt) REVERT: A 603 LYS cc_start: 0.5817 (tppt) cc_final: 0.5584 (tppt) REVERT: A 604 GLU cc_start: 0.6016 (pm20) cc_final: 0.5256 (pt0) REVERT: A 699 GLU cc_start: 0.5836 (tp30) cc_final: 0.5599 (mm-30) REVERT: A 798 ASP cc_start: 0.6524 (t0) cc_final: 0.6269 (t0) REVERT: A 817 ASP cc_start: 0.7599 (m-30) cc_final: 0.7264 (m-30) REVERT: A 900 ASP cc_start: 0.6834 (m-30) cc_final: 0.6575 (m-30) REVERT: B 71 LEU cc_start: 0.5071 (tp) cc_final: 0.4793 (tp) REVERT: B 77 LEU cc_start: 0.5106 (mm) cc_final: 0.4777 (tp) REVERT: B 98 GLN cc_start: 0.3539 (mm-40) cc_final: 0.3320 (mm-40) REVERT: B 110 VAL cc_start: 0.5704 (t) cc_final: 0.5426 (p) REVERT: C 21 MET cc_start: 0.6530 (ppp) cc_final: 0.6205 (ppp) REVERT: C 34 PHE cc_start: 0.6597 (m-10) cc_final: 0.6313 (m-80) REVERT: C 337 SER cc_start: 0.8676 (t) cc_final: 0.8385 (p) REVERT: C 380 ASN cc_start: 0.8346 (m-40) cc_final: 0.8045 (m-40) REVERT: C 381 ILE cc_start: 0.8348 (mt) cc_final: 0.8120 (mm) REVERT: C 950 GLU cc_start: 0.6243 (mm-30) cc_final: 0.5866 (mt-10) REVERT: D 116 TRP cc_start: 0.3351 (OUTLIER) cc_final: 0.2340 (m100) REVERT: E 23 TRP cc_start: 0.5725 (p90) cc_final: 0.5291 (t-100) REVERT: E 39 ILE cc_start: 0.7230 (tt) cc_final: 0.6973 (mt) REVERT: E 306 PHE cc_start: 0.7902 (m-80) cc_final: 0.7593 (m-10) REVERT: E 496 GLN cc_start: 0.7208 (mm110) cc_final: 0.6942 (mm-40) REVERT: E 503 LEU cc_start: 0.8020 (tp) cc_final: 0.7654 (tp) REVERT: E 1009 MET cc_start: 0.6376 (mmt) cc_final: 0.4241 (mtt) REVERT: E 1012 PHE cc_start: 0.7012 (m-10) cc_final: 0.6737 (m-10) REVERT: E 1033 VAL cc_start: 0.8891 (t) cc_final: 0.8655 (m) REVERT: F 54 LEU cc_start: 0.4217 (pp) cc_final: 0.3781 (mp) REVERT: F 82 ARG cc_start: 0.5697 (mtt90) cc_final: 0.5116 (ttp-110) REVERT: F 127 SER cc_start: 0.6256 (p) cc_final: 0.6049 (t) REVERT: F 172 LEU cc_start: 0.4141 (OUTLIER) cc_final: 0.3919 (mt) REVERT: F 182 LEU cc_start: 0.3875 (mt) cc_final: 0.3181 (tp) REVERT: G 21 MET cc_start: 0.6941 (pmm) cc_final: 0.5200 (pmm) REVERT: G 527 TYR cc_start: 0.7072 (m-10) cc_final: 0.6824 (m-10) REVERT: G 732 ILE cc_start: 0.6931 (mt) cc_final: 0.6653 (mt) REVERT: G 739 MET cc_start: 0.7624 (tpp) cc_final: 0.7275 (tpp) REVERT: G 1014 ILE cc_start: 0.8503 (pt) cc_final: 0.8276 (pt) REVERT: G 1021 HIS cc_start: 0.7699 (p-80) cc_final: 0.7175 (p-80) REVERT: H 86 LEU cc_start: 0.6917 (mt) cc_final: 0.6659 (mt) REVERT: H 131 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.4761 (mm) REVERT: H 198 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5796 (mp) REVERT: H 294 ARG cc_start: 0.5632 (mmt180) cc_final: 0.4659 (mtm110) outliers start: 77 outliers final: 50 residues processed: 577 average time/residue: 0.1753 time to fit residues: 168.9407 Evaluate side-chains 530 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 475 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 930 ASN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 880 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 198 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 171 optimal weight: 10.0000 chunk 433 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 415 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 430 optimal weight: 0.5980 chunk 215 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 337 optimal weight: 0.4980 chunk 189 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1021 HIS G 182 ASN G 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.185972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149345 restraints weight = 49859.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147221 restraints weight = 79372.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149465 restraints weight = 70502.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149445 restraints weight = 45457.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151997 restraints weight = 39990.334| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36828 Z= 0.122 Angle : 0.525 7.988 50032 Z= 0.265 Chirality : 0.040 0.235 5752 Planarity : 0.004 0.056 6304 Dihedral : 7.437 117.564 5064 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.70 % Allowed : 14.25 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 4520 helix: 1.04 (0.12), residues: 2016 sheet: -0.25 (0.28), residues: 420 loop : -0.47 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 218 TYR 0.017 0.001 TYR E 996 PHE 0.023 0.001 PHE E 692 TRP 0.016 0.001 TRP G 475 HIS 0.012 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00278 (36812) covalent geometry : angle 0.52482 (50000) SS BOND : bond 0.00158 ( 16) SS BOND : angle 0.43492 ( 32) hydrogen bonds : bond 0.03703 ( 1525) hydrogen bonds : angle 4.50313 ( 4179) *********************** 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 627 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 522 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5741 (tmm160) cc_final: 0.5304 (tmt170) REVERT: A 42 LEU cc_start: 0.8102 (tt) cc_final: 0.7860 (tp) REVERT: A 321 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: A 513 MET cc_start: 0.8486 (mmm) cc_final: 0.7698 (mmt) REVERT: A 897 ASP cc_start: 0.5301 (p0) cc_final: 0.5068 (p0) REVERT: A 924 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7618 (mmm) REVERT: B 71 LEU cc_start: 0.5072 (tp) cc_final: 0.4795 (tp) REVERT: B 77 LEU cc_start: 0.5109 (mm) cc_final: 0.4739 (tp) REVERT: B 98 GLN cc_start: 0.3701 (mm-40) cc_final: 0.3445 (mm-40) REVERT: B 110 VAL cc_start: 0.5717 (t) cc_final: 0.5440 (p) REVERT: C 34 PHE cc_start: 0.7113 (m-10) cc_final: 0.6889 (m-80) REVERT: C 216 GLN cc_start: 0.7749 (pp30) cc_final: 0.7512 (pp30) REVERT: C 337 SER cc_start: 0.8627 (t) cc_final: 0.8314 (p) REVERT: C 380 ASN cc_start: 0.8284 (m-40) cc_final: 0.7767 (m-40) REVERT: C 381 ILE cc_start: 0.8450 (mt) cc_final: 0.8177 (mm) REVERT: C 436 GLU cc_start: 0.6333 (tp30) cc_final: 0.6117 (tp30) REVERT: C 456 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8233 (mt) REVERT: C 815 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.5630 (mp) REVERT: D 116 TRP cc_start: 0.3115 (OUTLIER) cc_final: 0.1722 (m100) REVERT: E 23 TRP cc_start: 0.6038 (p90) cc_final: 0.5635 (t-100) REVERT: E 119 VAL cc_start: 0.8946 (t) cc_final: 0.8632 (p) REVERT: E 306 PHE cc_start: 0.8160 (m-80) cc_final: 0.7917 (m-80) REVERT: E 314 MET cc_start: 0.8436 (tmm) cc_final: 0.8174 (ttp) REVERT: E 396 THR cc_start: 0.8785 (p) cc_final: 0.8442 (t) REVERT: E 496 GLN cc_start: 0.7060 (mm110) cc_final: 0.6824 (mm-40) REVERT: E 516 PHE cc_start: 0.6430 (t80) cc_final: 0.5896 (t80) REVERT: E 1014 ILE cc_start: 0.7266 (mm) cc_final: 0.6928 (mm) REVERT: F 54 LEU cc_start: 0.4186 (OUTLIER) cc_final: 0.3490 (mp) REVERT: F 82 ARG cc_start: 0.5797 (mtt90) cc_final: 0.5068 (ttp-110) REVERT: F 127 SER cc_start: 0.6398 (p) cc_final: 0.6133 (t) REVERT: F 182 LEU cc_start: 0.4019 (mt) cc_final: 0.3229 (tp) REVERT: G 328 ASN cc_start: 0.6402 (OUTLIER) cc_final: 0.5456 (m110) REVERT: G 456 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7602 (mt) REVERT: G 527 TYR cc_start: 0.7134 (m-10) cc_final: 0.6903 (m-10) REVERT: G 732 ILE cc_start: 0.6922 (mt) cc_final: 0.6600 (mt) REVERT: G 779 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7256 (tt) REVERT: G 1014 ILE cc_start: 0.8502 (pt) cc_final: 0.8230 (pt) REVERT: G 1021 HIS cc_start: 0.7673 (p-80) cc_final: 0.7275 (p-80) REVERT: H 124 LEU cc_start: 0.5575 (tp) cc_final: 0.5357 (tt) REVERT: H 131 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4656 (mm) REVERT: H 147 ASN cc_start: 0.3654 (m-40) cc_final: 0.3404 (m-40) REVERT: H 294 ARG cc_start: 0.5789 (mmt180) cc_final: 0.4662 (mtm110) outliers start: 105 outliers final: 67 residues processed: 601 average time/residue: 0.2164 time to fit residues: 217.7440 Evaluate side-chains 537 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 460 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 244 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 512 SER Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 689 THR Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 328 ASN Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 579 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 878 ILE Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 949 LEU Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 387 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 251 optimal weight: 0.8980 chunk 212 optimal weight: 0.0670 chunk 455 optimal weight: 8.9990 chunk 85 optimal weight: 0.0370 chunk 165 optimal weight: 7.9990 chunk 347 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN A 816 GLN A1021 HIS ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147414 restraints weight = 49805.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145187 restraints weight = 71418.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.147537 restraints weight = 66521.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147436 restraints weight = 44312.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149293 restraints weight = 38995.395| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36828 Z= 0.112 Angle : 0.519 11.991 50032 Z= 0.259 Chirality : 0.040 0.209 5752 Planarity : 0.004 0.048 6304 Dihedral : 6.999 94.898 5064 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.75 % Allowed : 15.61 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.13), residues: 4520 helix: 1.11 (0.12), residues: 2012 sheet: -0.21 (0.28), residues: 412 loop : -0.52 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 938 TYR 0.014 0.001 TYR E 996 PHE 0.021 0.001 PHE E 511 TRP 0.016 0.001 TRP A 475 HIS 0.007 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00254 (36812) covalent geometry : angle 0.51928 (50000) SS BOND : bond 0.00147 ( 16) SS BOND : angle 0.39505 ( 32) hydrogen bonds : bond 0.03572 ( 1525) hydrogen bonds : angle 4.42312 ( 4179) *********************** 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 594 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 487 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.5751 (tmm160) cc_final: 0.5300 (tmt170) REVERT: A 42 LEU cc_start: 0.8066 (tt) cc_final: 0.7834 (tp) REVERT: A 321 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 513 MET cc_start: 0.8456 (mmm) cc_final: 0.7746 (mmt) REVERT: A 604 GLU cc_start: 0.5911 (pm20) cc_final: 0.5590 (tp30) REVERT: A 798 ASP cc_start: 0.6688 (t0) cc_final: 0.6376 (t0) REVERT: B 71 LEU cc_start: 0.5101 (tp) cc_final: 0.4824 (tp) REVERT: B 77 LEU cc_start: 0.5069 (mm) cc_final: 0.4694 (tp) REVERT: B 98 GLN cc_start: 0.3914 (mm-40) cc_final: 0.3660 (mm-40) REVERT: B 110 VAL cc_start: 0.5790 (t) cc_final: 0.5496 (p) REVERT: C 34 PHE cc_start: 0.7210 (m-10) cc_final: 0.7005 (m-80) REVERT: C 216 GLN cc_start: 0.7745 (pp30) cc_final: 0.7356 (pp30) REVERT: C 337 SER cc_start: 0.8639 (t) cc_final: 0.8312 (p) REVERT: C 436 GLU cc_start: 0.6370 (tp30) cc_final: 0.6013 (tp30) REVERT: C 815 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.5499 (mp) REVERT: D 116 TRP cc_start: 0.3052 (OUTLIER) cc_final: 0.1623 (m100) REVERT: D 218 ARG cc_start: 0.5554 (tpm170) cc_final: 0.5308 (mmp80) REVERT: E 23 TRP cc_start: 0.6146 (p90) cc_final: 0.5462 (t60) REVERT: E 306 PHE cc_start: 0.8224 (m-80) cc_final: 0.7995 (m-80) REVERT: E 396 THR cc_start: 0.8677 (p) cc_final: 0.8383 (t) REVERT: E 503 LEU cc_start: 0.8116 (tp) cc_final: 0.7791 (tp) REVERT: E 536 MET cc_start: 0.7978 (tpp) cc_final: 0.7604 (tpp) REVERT: E 798 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8125 (t0) REVERT: E 799 MET cc_start: 0.8509 (tpp) cc_final: 0.8262 (tpp) REVERT: E 1009 MET cc_start: 0.5434 (mmp) cc_final: 0.2955 (mtt) REVERT: E 1014 ILE cc_start: 0.7474 (mm) cc_final: 0.7118 (mm) REVERT: F 54 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.3934 (mp) REVERT: F 82 ARG cc_start: 0.5854 (mtt90) cc_final: 0.4990 (ttp-110) REVERT: F 127 SER cc_start: 0.6431 (p) cc_final: 0.6074 (t) REVERT: F 182 LEU cc_start: 0.3983 (mt) cc_final: 0.3207 (tp) REVERT: G 21 MET cc_start: 0.7272 (pmm) cc_final: 0.5215 (pmm) REVERT: G 456 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7653 (mt) REVERT: G 497 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8047 (t) REVERT: G 527 TYR cc_start: 0.7246 (m-10) cc_final: 0.6936 (m-10) REVERT: G 732 ILE cc_start: 0.7034 (mt) cc_final: 0.6718 (mt) REVERT: G 739 MET cc_start: 0.7462 (tpp) cc_final: 0.7145 (tpp) REVERT: G 778 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7126 (mt) REVERT: G 974 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.6990 (mtm180) REVERT: G 1014 ILE cc_start: 0.8503 (pt) cc_final: 0.8211 (pt) REVERT: G 1021 HIS cc_start: 0.7814 (p-80) cc_final: 0.7380 (p-80) REVERT: H 131 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4553 (mm) REVERT: H 198 LEU cc_start: 0.6044 (mp) cc_final: 0.5798 (mp) REVERT: H 294 ARG cc_start: 0.6068 (mmt180) cc_final: 0.4638 (mtm110) outliers start: 107 outliers final: 70 residues processed: 572 average time/residue: 0.2150 time to fit residues: 206.2062 Evaluate side-chains 529 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 450 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 812 ASP Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 745 ASN Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 755 VAL Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 778 ILE Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 878 ILE Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 402 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN A 471 ASN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 745 ASN ** G 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.183422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.145425 restraints weight = 49596.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144187 restraints weight = 73820.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146195 restraints weight = 67845.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146402 restraints weight = 43678.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148283 restraints weight = 37891.107| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36828 Z= 0.131 Angle : 0.542 12.204 50032 Z= 0.271 Chirality : 0.041 0.183 5752 Planarity : 0.004 0.048 6304 Dihedral : 6.766 63.801 5064 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 16.49 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4520 helix: 1.08 (0.12), residues: 1976 sheet: -0.44 (0.27), residues: 424 loop : -0.45 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 976 TYR 0.016 0.001 TYR E 996 PHE 0.024 0.001 PHE G1000 TRP 0.026 0.001 TRP A 694 HIS 0.008 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00306 (36812) covalent geometry : angle 0.54218 (50000) SS BOND : bond 0.00164 ( 16) SS BOND : angle 0.42812 ( 32) hydrogen bonds : bond 0.03769 ( 1525) hydrogen bonds : angle 4.45460 ( 4179) *********************** 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 601 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 486 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8099 (tt) cc_final: 0.7856 (tp) REVERT: A 214 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 321 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: A 513 MET cc_start: 0.8462 (mmm) cc_final: 0.7819 (mmt) REVERT: A 526 LYS cc_start: 0.7875 (tptp) cc_final: 0.7190 (ttmm) REVERT: A 699 GLU cc_start: 0.6051 (tp30) cc_final: 0.5799 (mm-30) REVERT: A 924 MET cc_start: 0.8008 (mmm) cc_final: 0.7423 (mmm) REVERT: B 71 LEU cc_start: 0.5203 (tp) cc_final: 0.4928 (tp) REVERT: B 77 LEU cc_start: 0.5081 (mm) cc_final: 0.4663 (tp) REVERT: B 98 GLN cc_start: 0.4023 (mm-40) cc_final: 0.3806 (mm110) REVERT: B 110 VAL cc_start: 0.5794 (t) cc_final: 0.5533 (p) REVERT: C 21 MET cc_start: 0.6460 (ppp) cc_final: 0.6103 (ttt) REVERT: C 34 PHE cc_start: 0.7569 (m-10) cc_final: 0.7341 (m-80) REVERT: C 337 SER cc_start: 0.8601 (t) cc_final: 0.8251 (p) REVERT: C 402 GLN cc_start: 0.8080 (tt0) cc_final: 0.7854 (tt0) REVERT: C 456 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8283 (mt) REVERT: C 815 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5538 (mp) REVERT: D 116 TRP cc_start: 0.3083 (OUTLIER) cc_final: 0.1682 (m100) REVERT: D 218 ARG cc_start: 0.5388 (tpm170) cc_final: 0.5174 (mmp80) REVERT: E 21 MET cc_start: 0.7069 (pmm) cc_final: 0.6594 (ptp) REVERT: E 23 TRP cc_start: 0.6273 (p90) cc_final: 0.5719 (t-100) REVERT: E 39 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7579 (mm) REVERT: E 216 GLN cc_start: 0.7294 (mp10) cc_final: 0.7069 (pp30) REVERT: E 306 PHE cc_start: 0.8332 (m-80) cc_final: 0.8104 (m-80) REVERT: E 536 MET cc_start: 0.8014 (tpp) cc_final: 0.7668 (tpp) REVERT: E 798 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8148 (t0) REVERT: E 799 MET cc_start: 0.8534 (tpp) cc_final: 0.8276 (tpp) REVERT: E 1009 MET cc_start: 0.5424 (mmp) cc_final: 0.3104 (mtt) REVERT: E 1012 PHE cc_start: 0.6813 (m-10) cc_final: 0.6329 (m-10) REVERT: E 1014 ILE cc_start: 0.7326 (mm) cc_final: 0.7027 (mm) REVERT: F 54 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.3859 (mp) REVERT: F 82 ARG cc_start: 0.5820 (mtt90) cc_final: 0.4893 (ttp-110) REVERT: F 127 SER cc_start: 0.6583 (p) cc_final: 0.6139 (t) REVERT: F 182 LEU cc_start: 0.4167 (mt) cc_final: 0.3461 (tp) REVERT: G 21 MET cc_start: 0.7414 (pmm) cc_final: 0.4979 (pmm) REVERT: G 30 MET cc_start: 0.7609 (mmm) cc_final: 0.7361 (mmm) REVERT: G 216 GLN cc_start: 0.7661 (pp30) cc_final: 0.7145 (pp30) REVERT: G 456 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7561 (mt) REVERT: G 497 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.7964 (t) REVERT: G 527 TYR cc_start: 0.7271 (m-10) cc_final: 0.6983 (m-10) REVERT: G 732 ILE cc_start: 0.7190 (mt) cc_final: 0.6753 (mt) REVERT: G 739 MET cc_start: 0.7510 (tpp) cc_final: 0.7111 (tpp) REVERT: G 778 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7314 (mt) REVERT: G 1014 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8231 (pt) REVERT: H 131 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4533 (mm) REVERT: H 198 LEU cc_start: 0.5843 (mp) cc_final: 0.5563 (mp) REVERT: H 294 ARG cc_start: 0.6198 (mmt180) cc_final: 0.4656 (mtm110) outliers start: 115 outliers final: 78 residues processed: 575 average time/residue: 0.2152 time to fit residues: 205.2627 Evaluate side-chains 534 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 443 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 778 ILE Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 792 VAL Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1014 ILE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 38 optimal weight: 9.9990 chunk 293 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 401 optimal weight: 7.9990 chunk 316 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 932 ASN G 328 ASN G 465 ASN H 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.181180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142831 restraints weight = 49646.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140771 restraints weight = 72900.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142988 restraints weight = 67465.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143458 restraints weight = 41721.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145232 restraints weight = 37045.845| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36828 Z= 0.160 Angle : 0.579 13.667 50032 Z= 0.290 Chirality : 0.042 0.175 5752 Planarity : 0.004 0.049 6304 Dihedral : 6.786 62.399 5064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.19 % Allowed : 17.26 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 4520 helix: 0.90 (0.12), residues: 1980 sheet: -0.66 (0.26), residues: 424 loop : -0.54 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 974 TYR 0.019 0.002 TYR E 996 PHE 0.031 0.002 PHE E 692 TRP 0.021 0.001 TRP A 694 HIS 0.009 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00378 (36812) covalent geometry : angle 0.57868 (50000) SS BOND : bond 0.00199 ( 16) SS BOND : angle 0.52237 ( 32) hydrogen bonds : bond 0.04110 ( 1525) hydrogen bonds : angle 4.56001 ( 4179) *********************** 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 605 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 481 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8070 (tt) cc_final: 0.7833 (tp) REVERT: A 172 ASN cc_start: 0.7559 (t0) cc_final: 0.7091 (m-40) REVERT: A 214 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 321 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: A 513 MET cc_start: 0.8541 (mmm) cc_final: 0.7906 (mmt) REVERT: A 603 LYS cc_start: 0.5944 (tppt) cc_final: 0.5736 (tppt) REVERT: A 604 GLU cc_start: 0.6109 (pm20) cc_final: 0.5441 (pt0) REVERT: A 789 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 71 LEU cc_start: 0.5174 (tp) cc_final: 0.4841 (tp) REVERT: B 77 LEU cc_start: 0.5149 (mm) cc_final: 0.4670 (tp) REVERT: B 98 GLN cc_start: 0.3899 (mm-40) cc_final: 0.3679 (mm110) REVERT: B 110 VAL cc_start: 0.5925 (t) cc_final: 0.5683 (p) REVERT: B 218 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5331 (ttt180) REVERT: C 34 PHE cc_start: 0.7739 (m-10) cc_final: 0.7495 (m-80) REVERT: C 337 SER cc_start: 0.8603 (t) cc_final: 0.8097 (p) REVERT: C 402 GLN cc_start: 0.8122 (tt0) cc_final: 0.7914 (tt0) REVERT: C 456 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8433 (mt) REVERT: C 603 LYS cc_start: 0.7109 (tppt) cc_final: 0.6517 (mmtp) REVERT: C 818 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6479 (ttpp) REVERT: C 935 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7430 (t) REVERT: E 21 MET cc_start: 0.7183 (pmm) cc_final: 0.6966 (ptp) REVERT: E 39 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7528 (mm) REVERT: E 234 LYS cc_start: 0.7972 (tttt) cc_final: 0.7729 (ttpp) REVERT: E 306 PHE cc_start: 0.8508 (m-80) cc_final: 0.8267 (m-80) REVERT: E 536 MET cc_start: 0.7952 (tpp) cc_final: 0.7700 (tpp) REVERT: E 798 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8158 (t0) REVERT: E 1009 MET cc_start: 0.5623 (mmp) cc_final: 0.3458 (mtt) REVERT: F 54 LEU cc_start: 0.4481 (OUTLIER) cc_final: 0.3970 (mp) REVERT: F 82 ARG cc_start: 0.5898 (mtt90) cc_final: 0.4986 (ttp-110) REVERT: F 127 SER cc_start: 0.6247 (p) cc_final: 0.5839 (t) REVERT: F 182 LEU cc_start: 0.4208 (mt) cc_final: 0.3540 (tp) REVERT: G 21 MET cc_start: 0.7427 (pmm) cc_final: 0.4958 (pmm) REVERT: G 216 GLN cc_start: 0.7859 (pp30) cc_final: 0.7435 (pp30) REVERT: G 367 ASP cc_start: 0.7806 (m-30) cc_final: 0.7343 (m-30) REVERT: G 456 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7639 (mt) REVERT: G 578 ARG cc_start: 0.5252 (mtm180) cc_final: 0.5043 (mmt-90) REVERT: G 778 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7324 (mt) REVERT: G 1014 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8156 (pt) REVERT: H 124 LEU cc_start: 0.5649 (tp) cc_final: 0.5294 (tp) REVERT: H 198 LEU cc_start: 0.5947 (mp) cc_final: 0.5716 (mp) REVERT: H 294 ARG cc_start: 0.6550 (mmt180) cc_final: 0.4954 (mtm110) outliers start: 124 outliers final: 90 residues processed: 580 average time/residue: 0.2223 time to fit residues: 215.5942 Evaluate side-chains 555 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 453 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 39 ILE Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 525 GLN Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 824 SER Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 290 CYS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 96 SER Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 449 ASN Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 778 ILE Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 792 VAL Chi-restraints excluded: chain G residue 825 LEU Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1014 ILE Chi-restraints excluded: chain G residue 1035 THR Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 219 HIS Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 217 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 181 optimal weight: 0.0570 chunk 278 optimal weight: 0.0020 chunk 410 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 445 optimal weight: 20.0000 chunk 250 optimal weight: 0.6980 chunk 366 optimal weight: 0.2980 chunk 332 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN A 509 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** C 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 693 HIS H 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.184380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146891 restraints weight = 49294.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145153 restraints weight = 72931.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147138 restraints weight = 66766.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147388 restraints weight = 40860.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149341 restraints weight = 36777.291| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36828 Z= 0.100 Angle : 0.534 13.359 50032 Z= 0.263 Chirality : 0.040 0.176 5752 Planarity : 0.004 0.081 6304 Dihedral : 6.331 59.420 5064 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.06 % Allowed : 19.32 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4520 helix: 1.13 (0.12), residues: 1976 sheet: -0.56 (0.27), residues: 416 loop : -0.47 (0.14), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 218 TYR 0.017 0.001 TYR C 762 PHE 0.022 0.001 PHE A 144 TRP 0.036 0.001 TRP A 694 HIS 0.006 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00210 (36812) covalent geometry : angle 0.53427 (50000) SS BOND : bond 0.00092 ( 16) SS BOND : angle 0.39962 ( 32) hydrogen bonds : bond 0.03409 ( 1525) hydrogen bonds : angle 4.37069 ( 4179) *********************** 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 558 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 478 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8095 (tt) cc_final: 0.7853 (tp) REVERT: A 172 ASN cc_start: 0.7552 (t0) cc_final: 0.7039 (m-40) REVERT: A 214 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8586 (mp) REVERT: A 321 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: A 513 MET cc_start: 0.8384 (mmm) cc_final: 0.7928 (mmt) REVERT: A 526 LYS cc_start: 0.7963 (tptp) cc_final: 0.7456 (mptp) REVERT: A 603 LYS cc_start: 0.5888 (tppt) cc_final: 0.5671 (tppt) REVERT: A 604 GLU cc_start: 0.6012 (pm20) cc_final: 0.5418 (pt0) REVERT: A 830 MET cc_start: 0.8484 (mmm) cc_final: 0.8189 (mmm) REVERT: A 924 MET cc_start: 0.7889 (mmm) cc_final: 0.7316 (mmm) REVERT: A 931 ASP cc_start: 0.7143 (p0) cc_final: 0.6934 (p0) REVERT: A 1009 MET cc_start: 0.5243 (mmp) cc_final: 0.4673 (tpt) REVERT: B 71 LEU cc_start: 0.5333 (tp) cc_final: 0.5058 (tp) REVERT: B 77 LEU cc_start: 0.5029 (mm) cc_final: 0.4631 (tp) REVERT: B 98 GLN cc_start: 0.4155 (mm-40) cc_final: 0.3945 (mm110) REVERT: B 110 VAL cc_start: 0.5778 (t) cc_final: 0.5517 (p) REVERT: B 230 LEU cc_start: 0.5594 (mt) cc_final: 0.4334 (tt) REVERT: C 34 PHE cc_start: 0.7626 (m-10) cc_final: 0.7335 (m-80) REVERT: C 186 ASP cc_start: 0.8085 (m-30) cc_final: 0.7793 (m-30) REVERT: C 337 SER cc_start: 0.8649 (t) cc_final: 0.8155 (p) REVERT: C 402 GLN cc_start: 0.8061 (tt0) cc_final: 0.7847 (tt0) REVERT: C 456 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8330 (mt) REVERT: C 603 LYS cc_start: 0.6970 (tppt) cc_final: 0.6428 (mmtp) REVERT: C 778 ILE cc_start: 0.7495 (mp) cc_final: 0.7256 (tt) REVERT: C 818 LYS cc_start: 0.6750 (ttpp) cc_final: 0.6471 (ttpp) REVERT: C 901 THR cc_start: 0.8082 (t) cc_final: 0.7794 (p) REVERT: C 935 THR cc_start: 0.7760 (p) cc_final: 0.7437 (t) REVERT: D 116 TRP cc_start: 0.2993 (OUTLIER) cc_final: 0.1475 (m100) REVERT: E 285 MET cc_start: 0.8951 (ptt) cc_final: 0.8660 (ptp) REVERT: E 306 PHE cc_start: 0.8471 (m-80) cc_final: 0.8204 (m-80) REVERT: E 536 MET cc_start: 0.7969 (tpp) cc_final: 0.7710 (tpp) REVERT: E 798 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8169 (t0) REVERT: E 799 MET cc_start: 0.8516 (tpp) cc_final: 0.8312 (tpp) REVERT: E 911 CYS cc_start: 0.7308 (m) cc_final: 0.7018 (m) REVERT: E 1009 MET cc_start: 0.5485 (mmp) cc_final: 0.3299 (mtt) REVERT: E 1012 PHE cc_start: 0.6606 (m-10) cc_final: 0.6105 (m-10) REVERT: F 54 LEU cc_start: 0.4395 (OUTLIER) cc_final: 0.4068 (mp) REVERT: F 82 ARG cc_start: 0.5908 (mtt90) cc_final: 0.4938 (ttp-110) REVERT: F 127 SER cc_start: 0.6220 (p) cc_final: 0.5928 (t) REVERT: F 182 LEU cc_start: 0.4116 (mt) cc_final: 0.3508 (tp) REVERT: G 23 TRP cc_start: 0.5939 (t60) cc_final: 0.5586 (t60) REVERT: G 30 MET cc_start: 0.7685 (mmm) cc_final: 0.7358 (mmm) REVERT: G 216 GLN cc_start: 0.7782 (pp30) cc_final: 0.7274 (pp30) REVERT: G 367 ASP cc_start: 0.7746 (m-30) cc_final: 0.7247 (m-30) REVERT: G 456 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7618 (mt) REVERT: G 476 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6796 (p0) REVERT: G 607 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6520 (mtt90) REVERT: G 692 PHE cc_start: 0.7413 (m-80) cc_final: 0.7047 (m-10) REVERT: G 732 ILE cc_start: 0.7335 (mt) cc_final: 0.6924 (mt) REVERT: H 124 LEU cc_start: 0.5664 (tp) cc_final: 0.5328 (tp) REVERT: H 294 ARG cc_start: 0.6545 (mmt180) cc_final: 0.4984 (mtm110) REVERT: H 296 ARG cc_start: 0.4960 (mtt90) cc_final: 0.4686 (mtm-85) outliers start: 80 outliers final: 58 residues processed: 541 average time/residue: 0.2270 time to fit residues: 204.1257 Evaluate side-chains 513 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 447 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 779 LEU Chi-restraints excluded: chain G residue 792 VAL Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 251 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 336 optimal weight: 0.5980 chunk 440 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142907 restraints weight = 49536.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140807 restraints weight = 72832.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143368 restraints weight = 64367.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143315 restraints weight = 41358.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146230 restraints weight = 36908.990| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 36828 Z= 0.146 Angle : 0.585 11.794 50032 Z= 0.289 Chirality : 0.041 0.196 5752 Planarity : 0.004 0.048 6304 Dihedral : 6.456 65.662 5064 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.31 % Allowed : 19.39 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.13), residues: 4520 helix: 0.98 (0.12), residues: 1976 sheet: -0.74 (0.26), residues: 424 loop : -0.54 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.018 0.001 TYR E 996 PHE 0.028 0.002 PHE E 511 TRP 0.036 0.002 TRP A 694 HIS 0.008 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00342 (36812) covalent geometry : angle 0.58489 (50000) SS BOND : bond 0.00182 ( 16) SS BOND : angle 0.50142 ( 32) hydrogen bonds : bond 0.03974 ( 1525) hydrogen bonds : angle 4.49653 ( 4179) *********************** 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 557 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 467 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.8062 (tt) cc_final: 0.7823 (tp) REVERT: A 172 ASN cc_start: 0.7603 (t0) cc_final: 0.7137 (m-40) REVERT: A 214 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 321 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7070 (mt-10) REVERT: A 513 MET cc_start: 0.8521 (mmm) cc_final: 0.7888 (mmt) REVERT: A 526 LYS cc_start: 0.8031 (tptp) cc_final: 0.7295 (ttmm) REVERT: A 603 LYS cc_start: 0.5970 (tppt) cc_final: 0.5744 (tppt) REVERT: A 604 GLU cc_start: 0.6173 (pm20) cc_final: 0.5509 (pt0) REVERT: A 1009 MET cc_start: 0.5288 (mmp) cc_final: 0.4767 (tpt) REVERT: B 71 LEU cc_start: 0.5306 (tp) cc_final: 0.5037 (tp) REVERT: B 77 LEU cc_start: 0.5129 (mm) cc_final: 0.4700 (tp) REVERT: B 110 VAL cc_start: 0.5919 (t) cc_final: 0.5644 (p) REVERT: B 218 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.5514 (ttt180) REVERT: C 34 PHE cc_start: 0.7799 (m-10) cc_final: 0.7542 (m-80) REVERT: C 186 ASP cc_start: 0.8155 (m-30) cc_final: 0.7829 (m-30) REVERT: C 337 SER cc_start: 0.8620 (t) cc_final: 0.8109 (p) REVERT: C 456 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8330 (mt) REVERT: C 603 LYS cc_start: 0.7083 (tppt) cc_final: 0.6492 (mmtp) REVERT: C 613 LYS cc_start: 0.4361 (tppt) cc_final: 0.3937 (mtmm) REVERT: C 818 LYS cc_start: 0.6972 (ttpp) cc_final: 0.6702 (ttpp) REVERT: C 901 THR cc_start: 0.8135 (t) cc_final: 0.7819 (p) REVERT: C 935 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7554 (t) REVERT: D 116 TRP cc_start: 0.3255 (OUTLIER) cc_final: 0.1702 (m100) REVERT: E 93 TRP cc_start: 0.7515 (p-90) cc_final: 0.7250 (p-90) REVERT: E 234 LYS cc_start: 0.7971 (tttt) cc_final: 0.7715 (ttpp) REVERT: E 306 PHE cc_start: 0.8564 (m-80) cc_final: 0.8306 (m-80) REVERT: E 536 MET cc_start: 0.8003 (tpp) cc_final: 0.7714 (tpp) REVERT: E 798 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8226 (t0) REVERT: E 1009 MET cc_start: 0.5634 (mmp) cc_final: 0.3541 (mtt) REVERT: E 1012 PHE cc_start: 0.6548 (m-10) cc_final: 0.5992 (m-10) REVERT: F 54 LEU cc_start: 0.4290 (OUTLIER) cc_final: 0.4049 (mp) REVERT: F 82 ARG cc_start: 0.5834 (mtt90) cc_final: 0.5044 (ttp-110) REVERT: F 127 SER cc_start: 0.6219 (p) cc_final: 0.5756 (t) REVERT: F 182 LEU cc_start: 0.4105 (mt) cc_final: 0.3510 (tp) REVERT: G 21 MET cc_start: 0.7556 (pmm) cc_final: 0.5629 (pmm) REVERT: G 23 TRP cc_start: 0.5991 (t60) cc_final: 0.5616 (t60) REVERT: G 216 GLN cc_start: 0.7847 (pp30) cc_final: 0.7318 (pp30) REVERT: G 367 ASP cc_start: 0.7837 (m-30) cc_final: 0.7419 (m-30) REVERT: G 456 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7732 (mt) REVERT: G 732 ILE cc_start: 0.7432 (mt) cc_final: 0.7054 (mt) REVERT: G 778 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7113 (mt) REVERT: H 124 LEU cc_start: 0.5640 (tp) cc_final: 0.5303 (tp) REVERT: H 294 ARG cc_start: 0.6637 (mmt180) cc_final: 0.4919 (mtm110) REVERT: H 296 ARG cc_start: 0.5028 (mtt90) cc_final: 0.4745 (mtm-85) outliers start: 90 outliers final: 70 residues processed: 541 average time/residue: 0.2272 time to fit residues: 202.7570 Evaluate side-chains 517 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 437 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 285 MET Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 736 ASN Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 778 ILE Chi-restraints excluded: chain G residue 792 VAL Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 878 ILE Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 48 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 351 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 453 optimal weight: 4.9990 chunk 390 optimal weight: 10.0000 chunk 416 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 307 optimal weight: 0.1980 chunk 169 optimal weight: 20.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN B 98 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.143192 restraints weight = 49504.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142725 restraints weight = 78489.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144026 restraints weight = 71252.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145333 restraints weight = 43377.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145745 restraints weight = 37459.212| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36828 Z= 0.172 Angle : 0.615 11.983 50032 Z= 0.305 Chirality : 0.043 0.217 5752 Planarity : 0.004 0.059 6304 Dihedral : 6.637 83.054 5064 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.29 % Allowed : 19.65 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.13), residues: 4520 helix: 0.83 (0.12), residues: 1972 sheet: -0.91 (0.26), residues: 424 loop : -0.65 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 201 TYR 0.020 0.002 TYR E 996 PHE 0.039 0.002 PHE C 144 TRP 0.035 0.002 TRP A 694 HIS 0.009 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00409 (36812) covalent geometry : angle 0.61470 (50000) SS BOND : bond 0.00216 ( 16) SS BOND : angle 0.53131 ( 32) hydrogen bonds : bond 0.04166 ( 1525) hydrogen bonds : angle 4.60974 ( 4179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9040 Ramachandran restraints generated. 4520 Oldfield, 0 Emsley, 4520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 463 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ASN cc_start: 0.7561 (t0) cc_final: 0.7109 (m-40) REVERT: A 321 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: A 513 MET cc_start: 0.8522 (mmm) cc_final: 0.7943 (mmt) REVERT: A 526 LYS cc_start: 0.8037 (tptp) cc_final: 0.7312 (ttmm) REVERT: A 603 LYS cc_start: 0.6192 (tppt) cc_final: 0.5969 (tppt) REVERT: A 604 GLU cc_start: 0.6143 (pm20) cc_final: 0.5813 (pt0) REVERT: A 830 MET cc_start: 0.8473 (mmm) cc_final: 0.8200 (mmm) REVERT: A 1009 MET cc_start: 0.5295 (mmp) cc_final: 0.4759 (tpt) REVERT: B 71 LEU cc_start: 0.5266 (tp) cc_final: 0.4968 (tp) REVERT: B 99 ARG cc_start: 0.5199 (tmm-80) cc_final: 0.4564 (ttt90) REVERT: B 110 VAL cc_start: 0.5930 (t) cc_final: 0.5675 (p) REVERT: B 218 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5537 (ttt180) REVERT: B 230 LEU cc_start: 0.5400 (mt) cc_final: 0.4153 (tt) REVERT: B 277 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 29 SER cc_start: 0.7986 (m) cc_final: 0.7295 (p) REVERT: C 186 ASP cc_start: 0.8120 (m-30) cc_final: 0.7790 (m-30) REVERT: C 337 SER cc_start: 0.8572 (t) cc_final: 0.8093 (p) REVERT: C 456 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8324 (mt) REVERT: C 603 LYS cc_start: 0.7056 (tppt) cc_final: 0.6459 (mmtp) REVERT: C 613 LYS cc_start: 0.4504 (tppt) cc_final: 0.4294 (mttp) REVERT: C 818 LYS cc_start: 0.6922 (ttpp) cc_final: 0.6594 (ttpp) REVERT: C 931 ASP cc_start: 0.6874 (p0) cc_final: 0.6616 (p0) REVERT: C 935 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7631 (t) REVERT: D 116 TRP cc_start: 0.3226 (OUTLIER) cc_final: 0.1783 (m100) REVERT: E 93 TRP cc_start: 0.7548 (p-90) cc_final: 0.7272 (p-90) REVERT: E 234 LYS cc_start: 0.8010 (tttt) cc_final: 0.7748 (ttpp) REVERT: E 523 THR cc_start: 0.7169 (p) cc_final: 0.6912 (m) REVERT: E 536 MET cc_start: 0.7988 (tpp) cc_final: 0.7712 (tpp) REVERT: E 799 MET cc_start: 0.8597 (tpp) cc_final: 0.8360 (tpp) REVERT: E 922 SER cc_start: 0.9101 (p) cc_final: 0.8396 (t) REVERT: E 1009 MET cc_start: 0.5365 (mmp) cc_final: 0.3356 (mtt) REVERT: E 1012 PHE cc_start: 0.6472 (m-10) cc_final: 0.5884 (m-10) REVERT: F 82 ARG cc_start: 0.5878 (mtt90) cc_final: 0.5164 (ttp-110) REVERT: F 127 SER cc_start: 0.6196 (p) cc_final: 0.5847 (t) REVERT: F 182 LEU cc_start: 0.4235 (mt) cc_final: 0.3697 (tp) REVERT: F 266 TYR cc_start: 0.7824 (m-10) cc_final: 0.7575 (m-80) REVERT: G 21 MET cc_start: 0.7361 (pmm) cc_final: 0.5363 (pmm) REVERT: G 23 TRP cc_start: 0.6108 (t60) cc_final: 0.5736 (t60) REVERT: G 30 MET cc_start: 0.7770 (mmm) cc_final: 0.7359 (mmm) REVERT: G 154 MET cc_start: 0.7837 (mmm) cc_final: 0.7570 (mmm) REVERT: G 216 GLN cc_start: 0.7910 (pp30) cc_final: 0.7386 (pp30) REVERT: G 367 ASP cc_start: 0.7873 (m-30) cc_final: 0.7471 (m-30) REVERT: G 456 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7747 (mt) REVERT: G 732 ILE cc_start: 0.7489 (mt) cc_final: 0.7135 (mt) REVERT: G 778 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7077 (mt) REVERT: H 124 LEU cc_start: 0.5834 (tp) cc_final: 0.5351 (tp) REVERT: H 294 ARG cc_start: 0.6695 (mmt180) cc_final: 0.5302 (mtp-110) outliers start: 89 outliers final: 71 residues processed: 542 average time/residue: 0.2193 time to fit residues: 195.7282 Evaluate side-chains 516 residues out of total 3892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 437 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1029 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 456 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 609 PHE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1000 PHE Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain E residue 755 VAL Chi-restraints excluded: chain E residue 798 ASP Chi-restraints excluded: chain E residue 886 THR Chi-restraints excluded: chain E residue 917 VAL Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain E residue 968 THR Chi-restraints excluded: chain E residue 1000 PHE Chi-restraints excluded: chain E residue 1022 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 200 ASN Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 404 SER Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain G residue 476 ASN Chi-restraints excluded: chain G residue 497 SER Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain G residue 609 PHE Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain G residue 778 ILE Chi-restraints excluded: chain G residue 792 VAL Chi-restraints excluded: chain G residue 872 THR Chi-restraints excluded: chain G residue 930 ASN Chi-restraints excluded: chain G residue 1000 PHE Chi-restraints excluded: chain G residue 1049 ILE Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 285 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 156 optimal weight: 0.1980 chunk 397 optimal weight: 6.9990 chunk 374 optimal weight: 0.0000 chunk 135 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 409 HIS A 471 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 471 ASN H 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147458 restraints weight = 49425.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.146098 restraints weight = 77179.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147691 restraints weight = 73709.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148215 restraints weight = 45730.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149233 restraints weight = 40976.526| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36828 Z= 0.103 Angle : 0.553 10.844 50032 Z= 0.273 Chirality : 0.040 0.260 5752 Planarity : 0.004 0.047 6304 Dihedral : 6.292 87.940 5064 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.95 % Allowed : 20.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.13), residues: 4520 helix: 1.08 (0.12), residues: 1972 sheet: -0.81 (0.26), residues: 416 loop : -0.58 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 938 TYR 0.014 0.001 TYR E 996 PHE 0.033 0.001 PHE C 144 TRP 0.033 0.001 TRP E 23 HIS 0.006 0.001 HIS E 254 Details of bonding type rmsd covalent geometry : bond 0.00226 (36812) covalent geometry : angle 0.55264 (50000) SS BOND : bond 0.00119 ( 16) SS BOND : angle 0.39218 ( 32) hydrogen bonds : bond 0.03475 ( 1525) hydrogen bonds : angle 4.41100 ( 4179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.01 seconds wall clock time: 104 minutes 51.54 seconds (6291.54 seconds total)