Starting phenix.real_space_refine on Thu Mar 21 10:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/03_2024/7vxb_32174.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 145 5.16 5 C 19069 2.51 5 N 5002 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29888 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8354 Classifications: {'peptide': 1068} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "A" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8354 Classifications: {'peptide': 1068} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 14.87, per 1000 atoms: 0.50 Number of scatterers: 29888 At special positions: 0 Unit cell: (161.764, 150.834, 239.367, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 145 16.00 O 5672 8.00 N 5002 7.00 C 19069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.76 Conformation dependent library (CDL) restraints added in 4.9 seconds 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 52 sheets defined 30.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.610A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.668A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.678A pdb=" N CYS D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.508A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 753 " --> pdb=" O CYS D 749 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 754 " --> pdb=" O SER D 750 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 780 removed outlier: 4.590A pdb=" N THR D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D 765 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.985A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 856 removed outlier: 3.694A pdb=" N GLN D 853 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 856 " --> pdb=" O ALA D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 removed outlier: 3.512A pdb=" N THR D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.709A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.718A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.974A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 3.573A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 removed outlier: 3.638A pdb=" N ASP D1146 " --> pdb=" O PRO D1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.553A pdb=" N GLN C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.564A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.948A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.811A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.965A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.963A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.617A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.692A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 194 removed outlier: 4.298A pdb=" N LEU C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.524A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 248 removed outlier: 4.060A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.559A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.131A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.711A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.625A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.565A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 399 through 413 removed outlier: 4.143A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.559A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.722A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 465 removed outlier: 3.961A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.937A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.107A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.824A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.654A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.770A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.793A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.669A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.809A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.778A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.173A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.800A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.509A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.617A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.763A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.063A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.545A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.579A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.605A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.604A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.605A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.768A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.864A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.636A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.820A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 removed outlier: 3.877A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 65 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 187 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 191 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.614A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.626A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 118 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D 129 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL D 126 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR D 170 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE D 128 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE D 168 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 130 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS D 166 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 164 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.551A pdb=" N LEU D 141 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.491A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'D' and resid 565 through 566 removed outlier: 6.844A pdb=" N PHE D 565 " --> pdb=" O PHE B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.502A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'D' and resid 788 through 789 removed outlier: 5.942A pdb=" N ILE D 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.660A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.445A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.725A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 359 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 35 through 37 removed outlier: 8.110A pdb=" N ASN A 68 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR A 269 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 267 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 54 through 62 removed outlier: 3.580A pdb=" N VAL A 54 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 60 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.044A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 83 through 85 removed outlier: 7.417A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.522A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.286A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.537A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AD8, first strand: chain 'A' and resid 807 through 808 removed outlier: 4.451A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.160A pdb=" N ALA B 34 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN B 68 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 269 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 267 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 55 through 62 removed outlier: 7.429A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.388A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.925A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.538A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.574A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.306A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'B' and resid 807 through 808 removed outlier: 4.117A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1120 through 1122 1169 hydrogen bonds defined for protein. 3276 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: 13.16 Time building geometry restraints manager: 11.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9686 1.35 - 1.47: 7578 1.47 - 1.59: 13141 1.59 - 1.71: 0 1.71 - 1.83: 196 Bond restraints: 30601 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.440 -0.106 2.34e-02 1.83e+03 2.06e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.411 -0.077 2.34e-02 1.83e+03 1.09e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.57e+00 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.08e+00 bond pdb=" N GLN A 21 " pdb=" CA GLN A 21 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 ... (remaining 30596 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 1035 107.32 - 113.99: 16927 113.99 - 120.66: 12230 120.66 - 127.33: 11112 127.33 - 134.00: 314 Bond angle restraints: 41618 Sorted by residual: angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 116.63 111.52 5.11 1.16e+00 7.43e-01 1.94e+01 angle pdb=" O PRO B 32 " pdb=" C PRO B 32 " pdb=" N PRO B 33 " ideal model delta sigma weight residual 121.15 122.80 -1.65 4.70e-01 4.53e+00 1.23e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.34 111.47 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" C ASN B 544 " pdb=" CA ASN B 544 " pdb=" CB ASN B 544 " ideal model delta sigma weight residual 110.42 116.02 -5.60 1.99e+00 2.53e-01 7.91e+00 angle pdb=" C LEU B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta sigma weight residual 119.66 121.56 -1.90 7.20e-01 1.93e+00 6.95e+00 ... (remaining 41613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 17820 16.05 - 32.10: 299 32.10 - 48.14: 86 48.14 - 64.19: 21 64.19 - 80.24: 5 Dihedral angle restraints: 18231 sinusoidal: 7171 harmonic: 11060 Sorted by residual: dihedral pdb=" SG CYS A 738 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " pdb=" CA CYS A 760 " ideal model delta sinusoidal sigma weight residual 79.00 5.94 73.06 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" SG CYS B 738 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " pdb=" CA CYS B 760 " ideal model delta sinusoidal sigma weight residual -73.00 -3.34 -69.66 1 2.00e+01 2.50e-03 1.57e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 18228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3077 0.030 - 0.060: 1052 0.060 - 0.090: 204 0.090 - 0.120: 264 0.120 - 0.150: 50 Chirality restraints: 4647 Sorted by residual: chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 4644 not shown) Planarity restraints: 5403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 31 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C LEU B 31 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 31 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 32 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 335 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 336 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 336 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 336 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 295 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.019 5.00e-02 4.00e+02 ... (remaining 5400 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 230 2.62 - 3.19: 26690 3.19 - 3.76: 43722 3.76 - 4.33: 63995 4.33 - 4.90: 104570 Nonbonded interactions: 239207 Sorted by model distance: nonbonded pdb=" OG SER D 813 " pdb=" OE1 GLU D 868 " model vdw 2.045 2.440 nonbonded pdb=" OG1 THR D 599 " pdb=" O GLN D 607 " model vdw 2.069 2.440 nonbonded pdb=" OG1 THR C 276 " pdb=" OG1 THR C 445 " model vdw 2.088 2.440 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLY A 219 " model vdw 2.101 2.440 nonbonded pdb=" OG SER D 98 " pdb=" O GLU D 180 " model vdw 2.126 2.440 ... (remaining 239202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 21 through 827 or resid 854 through 1147)) selection = (chain 'D' and (resid 14 through 827 or resid 854 through 1147)) } 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.970 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 77.250 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.150 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.106 30601 Z= 0.120 Angle : 0.406 5.596 41618 Z= 0.240 Chirality : 0.040 0.150 4647 Planarity : 0.002 0.036 5403 Dihedral : 7.201 80.240 10987 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 3757 helix: -2.05 (0.13), residues: 969 sheet: -0.78 (0.15), residues: 764 loop : -0.98 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 436 HIS 0.002 0.000 HIS C 535 PHE 0.016 0.001 PHE A 392 TYR 0.014 0.001 TYR A 145 ARG 0.002 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1034 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 269 TYR cc_start: 0.3838 (p90) cc_final: 0.3624 (p90) REVERT: D 456 PHE cc_start: 0.2979 (m-10) cc_final: 0.2460 (m-80) REVERT: D 1061 VAL cc_start: 0.8747 (t) cc_final: 0.8386 (t) REVERT: D 1118 ASP cc_start: 0.6913 (m-30) cc_final: 0.6687 (m-30) REVERT: C 117 ASN cc_start: 0.7601 (m-40) cc_final: 0.7007 (p0) REVERT: C 270 MET cc_start: 0.2884 (tpt) cc_final: 0.2136 (tpt) REVERT: C 305 GLN cc_start: 0.8231 (mt0) cc_final: 0.7731 (tm-30) REVERT: C 579 MET cc_start: 0.4014 (mtm) cc_final: 0.3554 (pmm) REVERT: A 62 PHE cc_start: 0.6784 (m-10) cc_final: 0.6537 (m-80) REVERT: A 81 ASN cc_start: 0.6770 (p0) cc_final: 0.6313 (p0) REVERT: A 598 ILE cc_start: 0.8061 (mt) cc_final: 0.7585 (mt) REVERT: A 805 ILE cc_start: 0.8446 (mt) cc_final: 0.8111 (mt) REVERT: A 816 SER cc_start: 0.7902 (p) cc_final: 0.7430 (t) REVERT: A 1012 LEU cc_start: 0.9202 (mt) cc_final: 0.8872 (mt) REVERT: B 582 LEU cc_start: 0.7677 (tp) cc_final: 0.6986 (tt) REVERT: B 730 SER cc_start: 0.8586 (t) cc_final: 0.8341 (p) outliers start: 0 outliers final: 0 residues processed: 1034 average time/residue: 0.4268 time to fit residues: 690.1160 Evaluate side-chains 500 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 0.0020 chunk 97 optimal weight: 2.9990 chunk 192 optimal weight: 0.0670 chunk 152 optimal weight: 0.0000 chunk 295 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 342 optimal weight: 6.9990 overall best weight: 0.3532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS D 69 HIS ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 394 ASN D 484 GLN D 641 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN D1106 GLN C 24 GLN C 103 ASN C 241 HIS C 401 HIS C 417 HIS C 508 ASN C 526 GLN A 59 GLN A 317 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 907 ASN A1005 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 856 ASN B 901 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30601 Z= 0.194 Angle : 0.618 11.146 41618 Z= 0.320 Chirality : 0.046 0.250 4647 Planarity : 0.004 0.035 5403 Dihedral : 3.813 22.372 4071 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 2.23 % Allowed : 10.93 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 3757 helix: 0.10 (0.15), residues: 1032 sheet: -0.17 (0.16), residues: 729 loop : -0.68 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 328 HIS 0.007 0.001 HIS D1048 PHE 0.029 0.002 PHE B 970 TYR 0.024 0.002 TYR A 741 ARG 0.006 0.001 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 543 time to evaluate : 3.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1034 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8865 (tt) REVERT: C 117 ASN cc_start: 0.7576 (m-40) cc_final: 0.7033 (p0) REVERT: C 121 ASN cc_start: 0.7122 (p0) cc_final: 0.6822 (p0) REVERT: C 152 MET cc_start: -0.2175 (ttm) cc_final: -0.2421 (ttm) REVERT: C 295 ASP cc_start: 0.7106 (m-30) cc_final: 0.6864 (p0) REVERT: C 305 GLN cc_start: 0.8139 (mt0) cc_final: 0.7796 (tm-30) REVERT: C 323 MET cc_start: -0.0407 (mmt) cc_final: -0.0741 (mmt) REVERT: C 383 MET cc_start: 0.7771 (mmm) cc_final: 0.7394 (ttp) REVERT: C 480 MET cc_start: 0.7307 (ppp) cc_final: 0.6936 (tmm) REVERT: A 223 LEU cc_start: 0.8314 (mp) cc_final: 0.7906 (mp) REVERT: A 816 SER cc_start: 0.7460 (p) cc_final: 0.7108 (t) REVERT: A 965 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8636 (tp40) REVERT: B 62 PHE cc_start: 0.7059 (m-10) cc_final: 0.6732 (m-10) REVERT: B 196 ASN cc_start: 0.6676 (m-40) cc_final: 0.6409 (m-40) REVERT: B 214 ARG cc_start: 0.4338 (OUTLIER) cc_final: 0.4068 (tpt170) REVERT: B 777 ASN cc_start: 0.8633 (m-40) cc_final: 0.8391 (t0) REVERT: B 870 ILE cc_start: 0.8260 (mt) cc_final: 0.8028 (mt) REVERT: B 1040 VAL cc_start: 0.7732 (t) cc_final: 0.7240 (t) outliers start: 74 outliers final: 41 residues processed: 594 average time/residue: 0.3756 time to fit residues: 362.3093 Evaluate side-chains 449 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 406 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 960 ASN Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.0980 chunk 106 optimal weight: 0.0170 chunk 284 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 3.9990 chunk 370 optimal weight: 0.7980 chunk 305 optimal weight: 9.9990 chunk 340 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 275 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN A 245 HIS A 360 ASN A 519 HIS A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 774 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 920 GLN B 965 GLN B1048 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30601 Z= 0.179 Angle : 0.573 11.405 41618 Z= 0.292 Chirality : 0.044 0.179 4647 Planarity : 0.004 0.042 5403 Dihedral : 3.878 18.401 4071 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 2.62 % Allowed : 13.04 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3757 helix: 0.71 (0.16), residues: 1018 sheet: 0.16 (0.17), residues: 713 loop : -0.63 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 71 HIS 0.005 0.001 HIS A1048 PHE 0.024 0.002 PHE B 970 TYR 0.024 0.001 TYR D 695 ARG 0.007 0.001 ARG D 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 450 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 980 ILE cc_start: 0.8899 (tp) cc_final: 0.8492 (mm) REVERT: D 1029 MET cc_start: 0.8110 (tpp) cc_final: 0.7878 (tpt) REVERT: D 1034 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8864 (tt) REVERT: D 1102 TRP cc_start: 0.8513 (m100) cc_final: 0.8117 (m100) REVERT: D 1135 ASN cc_start: 0.7267 (t0) cc_final: 0.6926 (m-40) REVERT: C 117 ASN cc_start: 0.7603 (m-40) cc_final: 0.7203 (p0) REVERT: C 250 ASN cc_start: 0.5527 (m-40) cc_final: 0.5125 (p0) REVERT: C 270 MET cc_start: 0.3747 (tpt) cc_final: 0.3478 (tpp) REVERT: C 298 VAL cc_start: 0.6595 (t) cc_final: 0.6235 (p) REVERT: C 305 GLN cc_start: 0.8113 (mt0) cc_final: 0.7687 (tm-30) REVERT: C 383 MET cc_start: 0.7836 (mmm) cc_final: 0.7454 (ttp) REVERT: A 62 PHE cc_start: 0.6285 (m-80) cc_final: 0.6020 (m-80) REVERT: A 100 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6536 (tp) REVERT: A 195 LYS cc_start: 0.8852 (pptt) cc_final: 0.8518 (pptt) REVERT: A 223 LEU cc_start: 0.8328 (mp) cc_final: 0.8022 (mp) REVERT: A 318 PHE cc_start: 0.5886 (t80) cc_final: 0.5676 (t80) REVERT: A 816 SER cc_start: 0.7539 (p) cc_final: 0.7026 (t) REVERT: A 965 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8430 (tp40) REVERT: B 196 ASN cc_start: 0.6925 (m-40) cc_final: 0.6645 (m-40) REVERT: B 214 ARG cc_start: 0.4916 (OUTLIER) cc_final: 0.4660 (tpt90) REVERT: B 823 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 864 LEU cc_start: 0.8524 (tp) cc_final: 0.8149 (tp) outliers start: 87 outliers final: 51 residues processed: 511 average time/residue: 0.3691 time to fit residues: 310.3097 Evaluate side-chains 433 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 378 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 795 LYS Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 344 optimal weight: 0.0020 chunk 364 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN D 207 HIS D 218 GLN D 655 HIS ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30601 Z= 0.214 Angle : 0.582 12.961 41618 Z= 0.300 Chirality : 0.044 0.300 4647 Planarity : 0.004 0.043 5403 Dihedral : 3.995 18.073 4071 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 3.01 % Allowed : 13.37 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 3757 helix: 0.91 (0.16), residues: 1024 sheet: 0.25 (0.18), residues: 687 loop : -0.56 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 258 HIS 0.031 0.001 HIS A 519 PHE 0.043 0.002 PHE B 275 TYR 0.018 0.002 TYR B 369 ARG 0.008 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 399 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1034 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8895 (tt) REVERT: C 117 ASN cc_start: 0.7534 (m-40) cc_final: 0.7111 (p0) REVERT: C 250 ASN cc_start: 0.5492 (m-40) cc_final: 0.5181 (p0) REVERT: C 270 MET cc_start: 0.4497 (tpt) cc_final: 0.4149 (tpp) REVERT: C 305 GLN cc_start: 0.7968 (mt0) cc_final: 0.7722 (tm-30) REVERT: A 195 LYS cc_start: 0.8698 (pptt) cc_final: 0.8408 (pptt) REVERT: A 730 SER cc_start: 0.9289 (p) cc_final: 0.8993 (t) REVERT: B 177 MET cc_start: 0.2418 (tmm) cc_final: -0.0445 (ptt) REVERT: B 196 ASN cc_start: 0.6994 (m-40) cc_final: 0.6749 (m-40) REVERT: B 740 MET cc_start: 0.8414 (tmm) cc_final: 0.7927 (tmm) REVERT: B 777 ASN cc_start: 0.9004 (m-40) cc_final: 0.8776 (t0) REVERT: B 964 LYS cc_start: 0.8337 (tppt) cc_final: 0.7676 (tppt) REVERT: B 965 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: B 1040 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8250 (m) outliers start: 100 outliers final: 61 residues processed: 470 average time/residue: 0.3710 time to fit residues: 288.7121 Evaluate side-chains 410 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 346 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 576 VAL Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 chunk 271 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 310 optimal weight: 0.6980 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN D 125 ASN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 ASN C 24 GLN A 519 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30601 Z= 0.193 Angle : 0.545 9.317 41618 Z= 0.280 Chirality : 0.043 0.190 4647 Planarity : 0.004 0.044 5403 Dihedral : 3.954 23.710 4071 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.75 % Rotamer: Outliers : 3.04 % Allowed : 14.48 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 3757 helix: 1.11 (0.16), residues: 1017 sheet: 0.37 (0.18), residues: 672 loop : -0.55 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 258 HIS 0.004 0.001 HIS A 519 PHE 0.036 0.001 PHE B 275 TYR 0.016 0.001 TYR B 741 ARG 0.010 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 385 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 737 ASP cc_start: 0.7600 (t0) cc_final: 0.7393 (t0) REVERT: C 117 ASN cc_start: 0.7537 (m-40) cc_final: 0.7130 (p0) REVERT: C 250 ASN cc_start: 0.5418 (m-40) cc_final: 0.5098 (p0) REVERT: C 270 MET cc_start: 0.4335 (tpt) cc_final: 0.0197 (mmt) REVERT: C 305 GLN cc_start: 0.8157 (mt0) cc_final: 0.7817 (tm-30) REVERT: A 62 PHE cc_start: 0.6264 (m-80) cc_final: 0.6011 (m-80) REVERT: A 104 TRP cc_start: 0.7073 (m-90) cc_final: 0.6735 (m-90) REVERT: A 195 LYS cc_start: 0.8612 (pptt) cc_final: 0.8351 (pptt) REVERT: A 223 LEU cc_start: 0.8250 (mp) cc_final: 0.7800 (mp) REVERT: A 290 ASP cc_start: 0.7540 (t0) cc_final: 0.7272 (p0) REVERT: A 674 TYR cc_start: 0.6422 (t80) cc_final: 0.5950 (t80) REVERT: A 731 MET cc_start: 0.7878 (pmm) cc_final: 0.7631 (ptt) REVERT: A 965 GLN cc_start: 0.8544 (tp40) cc_final: 0.8201 (tp-100) REVERT: B 177 MET cc_start: 0.2374 (tmm) cc_final: -0.0336 (ptt) REVERT: B 196 ASN cc_start: 0.6909 (m-40) cc_final: 0.6602 (m-40) REVERT: B 214 ARG cc_start: 0.5345 (OUTLIER) cc_final: 0.5113 (tpm170) REVERT: B 740 MET cc_start: 0.8313 (tmm) cc_final: 0.7783 (tmm) REVERT: B 776 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8337 (ttpp) REVERT: B 777 ASN cc_start: 0.8956 (m-40) cc_final: 0.8706 (t0) outliers start: 101 outliers final: 66 residues processed: 458 average time/residue: 0.4051 time to fit residues: 309.5548 Evaluate side-chains 408 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 340 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 9.9990 chunk 328 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 0.8980 chunk 302 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30601 Z= 0.179 Angle : 0.546 9.735 41618 Z= 0.280 Chirality : 0.043 0.263 4647 Planarity : 0.004 0.044 5403 Dihedral : 3.963 21.996 4071 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.01 % Favored : 96.91 % Rotamer: Outliers : 2.77 % Allowed : 15.75 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3757 helix: 1.15 (0.16), residues: 1027 sheet: 0.39 (0.18), residues: 675 loop : -0.57 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 258 HIS 0.004 0.001 HIS B1064 PHE 0.035 0.001 PHE B 275 TYR 0.020 0.001 TYR B 369 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 376 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 737 ASP cc_start: 0.7514 (t0) cc_final: 0.7172 (t0) REVERT: C 117 ASN cc_start: 0.7576 (m-40) cc_final: 0.7180 (p0) REVERT: C 250 ASN cc_start: 0.5541 (m-40) cc_final: 0.5216 (p0) REVERT: C 305 GLN cc_start: 0.8124 (mt0) cc_final: 0.7868 (tm-30) REVERT: A 62 PHE cc_start: 0.6265 (m-80) cc_final: 0.5997 (m-80) REVERT: A 195 LYS cc_start: 0.8604 (pptt) cc_final: 0.8361 (pptt) REVERT: A 223 LEU cc_start: 0.8180 (mp) cc_final: 0.7773 (mp) REVERT: A 515 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6194 (p90) REVERT: B 196 ASN cc_start: 0.7087 (m-40) cc_final: 0.6685 (m-40) REVERT: B 214 ARG cc_start: 0.5396 (OUTLIER) cc_final: 0.5143 (tpm170) REVERT: B 740 MET cc_start: 0.8352 (tmm) cc_final: 0.7731 (tmm) REVERT: B 776 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8389 (ttpp) REVERT: B 803 SER cc_start: 0.8051 (p) cc_final: 0.7691 (t) REVERT: B 970 PHE cc_start: 0.8253 (m-80) cc_final: 0.8029 (m-10) outliers start: 92 outliers final: 65 residues processed: 446 average time/residue: 0.3835 time to fit residues: 289.5530 Evaluate side-chains 409 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 341 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 782 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN D 498 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN D 969 ASN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 GLN A 474 GLN A 519 HIS A 536 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 30601 Z= 0.337 Angle : 0.684 9.702 41618 Z= 0.359 Chirality : 0.047 0.327 4647 Planarity : 0.005 0.086 5403 Dihedral : 4.615 24.638 4071 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 3.49 % Allowed : 15.60 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3757 helix: 0.76 (0.16), residues: 1044 sheet: 0.31 (0.18), residues: 721 loop : -0.75 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 258 HIS 0.010 0.001 HIS B1064 PHE 0.041 0.002 PHE B 275 TYR 0.022 0.002 TYR C 279 ARG 0.018 0.001 ARG D 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 370 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 714 ILE cc_start: 0.8933 (mt) cc_final: 0.8713 (mt) REVERT: D 748 GLU cc_start: 0.7344 (mp0) cc_final: 0.7089 (mp0) REVERT: D 779 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 117 ASN cc_start: 0.7616 (m-40) cc_final: 0.7137 (p0) REVERT: C 250 ASN cc_start: 0.5905 (m-40) cc_final: 0.5327 (p0) REVERT: C 305 GLN cc_start: 0.8353 (mt0) cc_final: 0.8000 (tm-30) REVERT: C 341 LYS cc_start: 0.4246 (OUTLIER) cc_final: 0.3363 (pttm) REVERT: A 21 GLN cc_start: 0.4511 (OUTLIER) cc_final: 0.3455 (mm-40) REVERT: A 515 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6006 (p90) REVERT: B 740 MET cc_start: 0.8455 (tmm) cc_final: 0.7834 (tmm) REVERT: B 803 SER cc_start: 0.7974 (p) cc_final: 0.7464 (t) REVERT: B 970 PHE cc_start: 0.8312 (m-80) cc_final: 0.8010 (m-80) outliers start: 116 outliers final: 79 residues processed: 457 average time/residue: 0.3595 time to fit residues: 276.8397 Evaluate side-chains 399 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 317 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 970 PHE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D 907 ASN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN A 519 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30601 Z= 0.177 Angle : 0.583 13.700 41618 Z= 0.296 Chirality : 0.044 0.349 4647 Planarity : 0.004 0.055 5403 Dihedral : 4.313 34.570 4071 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 2.47 % Allowed : 17.65 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3757 helix: 1.07 (0.16), residues: 1041 sheet: 0.35 (0.19), residues: 707 loop : -0.70 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 258 HIS 0.008 0.001 HIS A 56 PHE 0.035 0.002 PHE B 275 TYR 0.036 0.001 TYR D 365 ARG 0.007 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 361 time to evaluate : 3.324 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: D 223 LEU cc_start: 0.5894 (mm) cc_final: 0.5586 (mm) REVERT: D 549 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7733 (p) REVERT: D 774 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8408 (mm-40) REVERT: D 779 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 823 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: C 117 ASN cc_start: 0.7551 (m-40) cc_final: 0.7178 (p0) REVERT: C 250 ASN cc_start: 0.5870 (m-40) cc_final: 0.5327 (p0) REVERT: C 305 GLN cc_start: 0.8366 (mt0) cc_final: 0.7989 (tm-30) REVERT: A 62 PHE cc_start: 0.6788 (m-80) cc_final: 0.6491 (m-80) REVERT: A 104 TRP cc_start: 0.7514 (m-90) cc_final: 0.7206 (m-90) REVERT: A 223 LEU cc_start: 0.8242 (mp) cc_final: 0.7795 (mp) REVERT: A 515 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.5802 (p90) REVERT: B 740 MET cc_start: 0.8421 (tmm) cc_final: 0.8037 (tmm) outliers start: 82 outliers final: 67 residues processed: 419 average time/residue: 0.3547 time to fit residues: 251.5642 Evaluate side-chains 400 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 330 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 823 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 0.9990 chunk 317 optimal weight: 7.9990 chunk 338 optimal weight: 0.1980 chunk 203 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 265 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 0.0980 chunk 320 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 920 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN A 484 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30601 Z= 0.160 Angle : 0.579 13.751 41618 Z= 0.292 Chirality : 0.044 0.333 4647 Planarity : 0.004 0.061 5403 Dihedral : 4.152 27.440 4071 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.17 % Allowed : 18.49 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 3757 helix: 1.16 (0.16), residues: 1051 sheet: 0.48 (0.19), residues: 687 loop : -0.69 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 258 HIS 0.008 0.001 HIS A 519 PHE 0.040 0.001 PHE D 541 TYR 0.028 0.001 TYR D 365 ARG 0.005 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 360 time to evaluate : 2.814 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: D 386 LYS cc_start: 0.8142 (pttt) cc_final: 0.7695 (ptmm) REVERT: D 774 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8377 (mm-40) REVERT: D 823 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.7014 (m-10) REVERT: C 117 ASN cc_start: 0.7609 (m-40) cc_final: 0.7212 (p0) REVERT: C 250 ASN cc_start: 0.5817 (m-40) cc_final: 0.5272 (p0) REVERT: C 305 GLN cc_start: 0.8329 (mt0) cc_final: 0.7999 (tm-30) REVERT: C 332 MET cc_start: -0.0417 (mmm) cc_final: -0.0683 (mmm) REVERT: A 62 PHE cc_start: 0.6666 (m-80) cc_final: 0.6306 (m-80) REVERT: A 104 TRP cc_start: 0.7436 (m-90) cc_final: 0.7202 (m-90) REVERT: A 223 LEU cc_start: 0.8134 (mp) cc_final: 0.7734 (mp) REVERT: A 515 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.5877 (p90) REVERT: A 708 SER cc_start: 0.8289 (t) cc_final: 0.7741 (m) REVERT: B 177 MET cc_start: 0.2341 (ppp) cc_final: 0.0935 (ppp) REVERT: B 1034 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7870 (mt) outliers start: 72 outliers final: 56 residues processed: 414 average time/residue: 0.3578 time to fit residues: 250.3336 Evaluate side-chains 390 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 331 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 375 optimal weight: 3.9990 chunk 345 optimal weight: 0.0470 chunk 299 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 231 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30601 Z= 0.153 Angle : 0.581 14.012 41618 Z= 0.291 Chirality : 0.044 0.292 4647 Planarity : 0.004 0.044 5403 Dihedral : 4.092 26.491 4071 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 2.02 % Allowed : 18.82 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3757 helix: 1.18 (0.16), residues: 1062 sheet: 0.45 (0.19), residues: 680 loop : -0.66 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 258 HIS 0.006 0.001 HIS D 146 PHE 0.041 0.001 PHE B 275 TYR 0.023 0.001 TYR D 365 ARG 0.004 0.000 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 369 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 386 LYS cc_start: 0.8034 (pttt) cc_final: 0.7541 (ttmt) REVERT: D 774 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8401 (mm-40) REVERT: D 823 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6924 (m-10) REVERT: C 117 ASN cc_start: 0.7585 (m-40) cc_final: 0.7189 (p0) REVERT: C 250 ASN cc_start: 0.5801 (m-40) cc_final: 0.5273 (p0) REVERT: C 305 GLN cc_start: 0.8334 (mt0) cc_final: 0.7997 (tm-30) REVERT: A 62 PHE cc_start: 0.6553 (m-80) cc_final: 0.6128 (m-80) REVERT: A 104 TRP cc_start: 0.7308 (m-90) cc_final: 0.7093 (m-90) REVERT: A 223 LEU cc_start: 0.8122 (mp) cc_final: 0.7703 (mp) REVERT: A 515 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.5908 (p90) REVERT: B 177 MET cc_start: 0.2852 (ppp) cc_final: 0.1211 (ppp) REVERT: B 699 LEU cc_start: 0.7728 (mt) cc_final: 0.7527 (mt) outliers start: 67 outliers final: 59 residues processed: 416 average time/residue: 0.3712 time to fit residues: 259.7491 Evaluate side-chains 399 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 338 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 360 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 738 CYS Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 976 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 501 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 196 ASN B 207 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1064 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.124887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093352 restraints weight = 109926.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093858 restraints weight = 70250.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.094243 restraints weight = 48550.313| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.8061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 30601 Z= 0.484 Angle : 0.821 11.945 41618 Z= 0.432 Chirality : 0.050 0.355 4647 Planarity : 0.005 0.070 5403 Dihedral : 5.191 24.792 4071 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.59 % Allowed : 18.43 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3757 helix: 0.42 (0.15), residues: 1061 sheet: -0.05 (0.19), residues: 724 loop : -1.05 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP D 258 HIS 0.013 0.002 HIS B1064 PHE 0.052 0.003 PHE B 275 TYR 0.034 0.003 TYR A 380 ARG 0.012 0.001 ARG A 273 =============================================================================== Job complete usr+sys time: 6653.80 seconds wall clock time: 120 minutes 44.48 seconds (7244.48 seconds total)