Starting phenix.real_space_refine (version: dev) on Mon Feb 27 10:28:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/02_2023/7vxb_32174.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/02_2023/7vxb_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_32174/02_2023/7vxb_32174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/02_2023/7vxb_32174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/02_2023/7vxb_32174.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vxb_32174/02_2023/7vxb_32174.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 16.25, per 1000 atoms: 0.54 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: 11.43 Conformation dependent library (CDL) restraints added in 4.4 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: 2.25 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: 12.94 Time building geometry restraints manager: 12.25 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 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. 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: 1.940 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: 11.920 Check model and map are aligned: 0.450 Process input model: 76.320 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 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 : 12.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 3.548 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 outliers start: 0 outliers final: 0 residues processed: 1034 average time/residue: 0.4456 time to fit residues: 720.8685 Evaluate side-chains 492 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 3.536 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8921 ------------------------------------------------------------------------------- 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: 3.9990 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 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 30601 Z= 0.188 Angle : 0.614 10.764 41618 Z= 0.320 Chirality : 0.045 0.242 4647 Planarity : 0.004 0.035 5403 Dihedral : 3.786 22.549 4071 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.82 % Rotamer Outliers : 2.23 % 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: -0.59 (0.12), residues: 3757 helix: 0.15 (0.15), residues: 1024 sheet: -0.18 (0.16), residues: 730 loop : -0.69 (0.12), residues: 2003 *********************** 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 610 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 536 time to evaluate : 3.483 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 outliers start: 74 outliers final: 42 residues processed: 585 average time/residue: 0.4080 time to fit residues: 386.6007 Evaluate side-chains 439 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 397 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2842 time to fit residues: 27.0424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 chunk 370 optimal weight: 0.4980 chunk 305 optimal weight: 4.9990 chunk 340 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN A 245 HIS A 360 ASN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN B 965 GLN B1048 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4657 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= 0.186 Angle : 0.583 11.822 41618 Z= 0.297 Chirality : 0.044 0.178 4647 Planarity : 0.004 0.042 5403 Dihedral : 3.955 22.176 4071 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer Outliers : 1.99 % 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: -0.18 (0.13), residues: 3757 helix: 0.65 (0.16), residues: 1029 sheet: 0.19 (0.17), residues: 725 loop : -0.59 (0.13), residues: 2003 *********************** 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 524 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 458 time to evaluate : 3.679 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 outliers start: 66 outliers final: 31 residues processed: 498 average time/residue: 0.4000 time to fit residues: 329.7042 Evaluate side-chains 399 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 368 time to evaluate : 3.438 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2877 time to fit residues: 20.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 344 optimal weight: 0.8980 chunk 364 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 326 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 207 HIS D 655 HIS ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 856 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 901 GLN ** 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: 0.6794 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 30601 Z= 0.184 Angle : 0.558 10.638 41618 Z= 0.287 Chirality : 0.043 0.224 4647 Planarity : 0.004 0.041 5403 Dihedral : 3.939 18.867 4071 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer Outliers : 1.32 % 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: -0.01 (0.13), residues: 3757 helix: 0.90 (0.16), residues: 1021 sheet: 0.27 (0.18), residues: 708 loop : -0.53 (0.13), residues: 2028 *********************** 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 440 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 396 time to evaluate : 3.411 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 outliers start: 44 outliers final: 24 residues processed: 426 average time/residue: 0.4098 time to fit residues: 289.9221 Evaluate side-chains 362 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 338 time to evaluate : 3.634 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2897 time to fit residues: 18.1007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 271 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 310 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 327 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 30601 Z= 0.254 Angle : 0.580 9.720 41618 Z= 0.301 Chirality : 0.044 0.239 4647 Planarity : 0.004 0.045 5403 Dihedral : 4.097 26.391 4071 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer Outliers : 1.63 % 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: 1.01 (0.16), residues: 1031 sheet: 0.31 (0.18), residues: 707 loop : -0.57 (0.13), residues: 2019 *********************** 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 440 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 386 time to evaluate : 3.952 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 outliers start: 54 outliers final: 29 residues processed: 415 average time/residue: 0.4386 time to fit residues: 306.5454 Evaluate side-chains 356 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 4.008 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3207 time to fit residues: 22.6088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 72 optimal weight: 4.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 364 optimal weight: 5.9990 chunk 302 optimal weight: 0.0770 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 120 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 overall best weight: 1.4478 ------------------------------------------------------------------------------- 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 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** 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** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 30601 Z= 0.195 Angle : 0.553 9.129 41618 Z= 0.287 Chirality : 0.043 0.286 4647 Planarity : 0.004 0.045 5403 Dihedral : 4.086 26.397 4071 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer Outliers : 1.32 % 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: 1.05 (0.16), residues: 1035 sheet: 0.38 (0.18), residues: 696 loop : -0.57 (0.13), residues: 2026 *********************** 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 415 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 371 time to evaluate : 3.964 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 outliers start: 44 outliers final: 24 residues processed: 395 average time/residue: 0.3830 time to fit residues: 257.3953 Evaluate side-chains 350 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 326 time to evaluate : 3.729 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2945 time to fit residues: 18.1761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 203 optimal weight: 0.4980 chunk 363 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN C 103 ASN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** 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** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** 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: 0.7050 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 30601 Z= 0.259 Angle : 0.604 9.261 41618 Z= 0.316 Chirality : 0.045 0.218 4647 Planarity : 0.004 0.064 5403 Dihedral : 4.332 21.136 4071 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer Outliers : 1.72 % 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: -0.08 (0.13), residues: 3757 helix: 0.93 (0.16), residues: 1048 sheet: 0.27 (0.18), residues: 685 loop : -0.67 (0.13), residues: 2024 *********************** 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 426 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 369 time to evaluate : 3.555 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 outliers start: 57 outliers final: 32 residues processed: 412 average time/residue: 0.3992 time to fit residues: 275.6004 Evaluate side-chains 356 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 3.509 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2746 time to fit residues: 21.2331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 217 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 247 optimal weight: 0.3980 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN ** D 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 ASN D 856 ASN D 907 ASN D 920 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN A 519 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30601 Z= 0.166 Angle : 0.554 8.144 41618 Z= 0.286 Chirality : 0.043 0.203 4647 Planarity : 0.004 0.040 5403 Dihedral : 4.166 28.184 4071 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.81 % Rotamer Outliers : 0.72 % 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: 1.12 (0.16), residues: 1046 sheet: 0.37 (0.19), residues: 688 loop : -0.62 (0.13), residues: 2023 *********************** 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 402 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 378 time to evaluate : 3.271 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 outliers start: 24 outliers final: 15 residues processed: 388 average time/residue: 0.3864 time to fit residues: 255.0289 Evaluate side-chains 349 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 334 time to evaluate : 3.705 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3033 time to fit residues: 13.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 chunk 317 optimal weight: 0.5980 chunk 338 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 0.0770 chunk 320 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 969 ASN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 30601 Z= 0.160 Angle : 0.572 11.684 41618 Z= 0.292 Chirality : 0.043 0.292 4647 Planarity : 0.004 0.048 5403 Dihedral : 4.076 27.203 4071 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer Outliers : 0.51 % 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: 0.12 (0.13), residues: 3757 helix: 1.13 (0.16), residues: 1062 sheet: 0.42 (0.19), residues: 666 loop : -0.57 (0.13), residues: 2029 *********************** 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 389 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 372 time to evaluate : 3.646 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 outliers start: 17 outliers final: 9 residues processed: 381 average time/residue: 0.4096 time to fit residues: 261.2261 Evaluate side-chains 351 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 342 time to evaluate : 3.660 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3492 time to fit residues: 10.5765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.1980 chunk 358 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 0.0030 chunk 248 optimal weight: 0.9990 chunk 375 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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** C 102 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 30601 Z= 0.163 Angle : 0.581 11.481 41618 Z= 0.296 Chirality : 0.044 0.322 4647 Planarity : 0.004 0.059 5403 Dihedral : 4.056 27.319 4071 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer Outliers : 0.39 % 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: 0.16 (0.13), residues: 3757 helix: 1.15 (0.16), residues: 1048 sheet: 0.47 (0.19), residues: 674 loop : -0.55 (0.13), residues: 2035 ********************** 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 376 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 363 time to evaluate : 4.026 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 outliers start: 13 outliers final: 8 residues processed: 368 average time/residue: 0.4009 time to fit residues: 249.9185 Evaluate side-chains 343 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 335 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3258 time to fit residues: 9.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 501 ASN ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 519 HIS ** 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 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 ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.127605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096628 restraints weight = 111526.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098020 restraints weight = 66082.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.098411 restraints weight = 43849.228| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.7923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.104 30601 Z= 0.460 Angle : 0.811 15.269 41618 Z= 0.427 Chirality : 0.050 0.379 4647 Planarity : 0.005 0.075 5403 Dihedral : 5.099 24.269 4071 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % Rotamer Outliers : 0.78 % 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: -0.50 (0.13), residues: 3757 helix: 0.53 (0.16), residues: 1052 sheet: 0.14 (0.19), residues: 693 loop : -0.95 (0.13), residues: 2012 =============================================================================== Job complete usr+sys time: 6560.66 seconds wall clock time: 120 minutes 28.18 seconds (7228.18 seconds total)