Starting phenix.real_space_refine on Sat Feb 7 21:08:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lul_63397/02_2026/9lul_63397.map" } resolution = 4.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 21604 2.51 5 N 7062 2.21 5 O 6995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35663 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2172 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 377} Link IDs: {'PTRANS': 8, 'TRANS': 425} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1375 Unresolved non-hydrogen angles: 1759 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 20, 'TRP:plan': 9, 'GLN:plan1': 19, 'PHE:plan': 17, 'ASP:plan': 27, 'ASN:plan1': 23, 'GLU:plan': 24, 'TYR:plan': 20} Unresolved non-hydrogen planarities: 800 Chain: "I" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2255 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 364} Link IDs: {'PTRANS': 8, 'TRANS': 425} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1280 Unresolved non-hydrogen angles: 1634 Unresolved non-hydrogen dihedrals: 1073 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 19, 'TRP:plan': 7, 'GLN:plan1': 19, 'PHE:plan': 12, 'ASP:plan': 27, 'ASN:plan1': 23, 'GLU:plan': 24, 'TYR:plan': 17} Unresolved non-hydrogen planarities: 726 Chain: "K" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 2655 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 467} Link IDs: {'PTRANS': 10, 'TRANS': 518} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1684 Unresolved non-hydrogen angles: 2144 Unresolved non-hydrogen dihedrals: 1421 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLU:plan': 37, 'ASP:plan': 35, 'ASN:plan1': 30, 'PHE:plan': 23, 'TYR:plan': 24, 'HIS:plan': 14, 'GLN:plan1': 22, 'ARG:plan': 23, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 985 Chain: "L" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 305 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 91 Chain: "M" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 2472 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 436} Link IDs: {'PTRANS': 11, 'TRANS': 481} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1587 Unresolved non-hydrogen angles: 2021 Unresolved non-hydrogen dihedrals: 1345 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'ASN:plan1': 26, 'ASP:plan': 29, 'PHE:plan': 23, 'GLU:plan': 35, 'TYR:plan': 23, 'HIS:plan': 13, 'GLN:plan1': 20, 'ARG:plan': 22, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 922 Chain: "N" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 2651 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 467} Link IDs: {'PTRANS': 10, 'TRANS': 518} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1690 Unresolved non-hydrogen angles: 2154 Unresolved non-hydrogen dihedrals: 1430 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLU:plan': 37, 'ASP:plan': 35, 'ASN:plan1': 30, 'PHE:plan': 24, 'TYR:plan': 24, 'HIS:plan': 13, 'GLN:plan1': 22, 'ARG:plan': 22, 'TRP:plan': 8} Unresolved non-hydrogen planarities: 990 Chain: "O" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 2465 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 437} Link IDs: {'PTRANS': 11, 'TRANS': 481} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1595 Unresolved non-hydrogen angles: 2032 Unresolved non-hydrogen dihedrals: 1353 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'ASN:plan1': 26, 'ASP:plan': 29, 'PHE:plan': 23, 'GLU:plan': 35, 'TYR:plan': 24, 'HIS:plan': 13, 'GLN:plan1': 20, 'ARG:plan': 22, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 929 Chain: "W" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 2220 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1422 Unresolved non-hydrogen angles: 1817 Unresolved non-hydrogen dihedrals: 1207 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 21, 'TRP:plan': 9, 'GLN:plan1': 20, 'PHE:plan': 17, 'ASP:plan': 27, 'ASN:plan1': 22, 'GLU:plan': 29, 'TYR:plan': 20} Unresolved non-hydrogen planarities: 826 Chain: "X" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 2220 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 390} Link IDs: {'PTRANS': 8, 'TRANS': 436} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1422 Unresolved non-hydrogen angles: 1817 Unresolved non-hydrogen dihedrals: 1207 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 21, 'TRP:plan': 9, 'GLN:plan1': 20, 'PHE:plan': 17, 'ASP:plan': 27, 'ASN:plan1': 22, 'GLU:plan': 29, 'TYR:plan': 20} Unresolved non-hydrogen planarities: 826 Chain: "a" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 794 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 133} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 307 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 5, 'ARG:plan': 6, 'PHE:plan': 5, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 198 Chain: "c" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 4115 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 694} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 795} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 2442 Unresolved non-hydrogen angles: 3130 Unresolved non-hydrogen dihedrals: 1984 Unresolved non-hydrogen chiralities: 251 Planarities with less than four sites: {'TYR:plan': 28, 'ASN:plan1': 39, 'GLN:plan1': 33, 'HIS:plan': 19, 'PHE:plan': 33, 'GLU:plan': 70, 'ASP:plan': 40, 'ARG:plan': 35, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 1358 Chain: "d" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 775 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 133} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 398 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 5, 'PHE:plan': 5, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "f" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 4109 Classifications: {'peptide': 822} Incomplete info: {'truncation_to_alanine': 695} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 794} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 2444 Unresolved non-hydrogen angles: 3130 Unresolved non-hydrogen dihedrals: 1986 Unresolved non-hydrogen chiralities: 250 Planarities with less than four sites: {'TYR:plan': 27, 'ASN:plan1': 39, 'GLN:plan1': 33, 'HIS:plan': 19, 'PHE:plan': 33, 'GLU:plan': 70, 'ASP:plan': 40, 'ARG:plan': 36, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 1356 Chain: "h" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "b" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 2989 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 384} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 499} Chain breaks: 1 Unresolved non-hydrogen bonds: 1362 Unresolved non-hydrogen angles: 1742 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'ARG:plan': 35, 'ASN:plan1': 22, 'GLN:plan1': 22, 'HIS:plan': 11, 'GLU:plan': 28, 'PHE:plan': 25, 'ASP:plan': 27, 'TYR:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 815 Chain: "e" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3065 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 393} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 515} Chain breaks: 1 Unresolved non-hydrogen bonds: 1415 Unresolved non-hydrogen angles: 1813 Unresolved non-hydrogen dihedrals: 1147 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'ARG:plan': 37, 'GLN:plan1': 22, 'ASN:plan1': 23, 'HIS:plan': 14, 'GLU:plan': 28, 'PHE:plan': 26, 'ASP:plan': 28, 'TYR:plan': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 866 Time building chain proxies: 9.79, per 1000 atoms: 0.27 Number of scatterers: 35663 At special positions: 0 Unit cell: (323, 259.25, 109.65, 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 2 16.00 O 6995 8.00 N 7062 7.00 C 21604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.1 seconds 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13134 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 114 sheets defined 26.1% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'H' and resid 218 through 230 removed outlier: 3.799A pdb=" N THR H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 284 Processing helix chain 'H' and resid 348 through 363 Processing helix chain 'H' and resid 363 through 376 Processing helix chain 'H' and resid 381 through 400 removed outlier: 3.622A pdb=" N THR H 385 " --> pdb=" O ASP H 381 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA H 386 " --> pdb=" O ASP H 382 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER H 387 " --> pdb=" O SER H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 456 Processing helix chain 'I' and resid 218 through 230 removed outlier: 3.960A pdb=" N THR I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 284 Processing helix chain 'I' and resid 348 through 363 Processing helix chain 'I' and resid 363 through 376 Processing helix chain 'I' and resid 381 through 400 removed outlier: 3.698A pdb=" N THR I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA I 386 " --> pdb=" O ASP I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 456 Processing helix chain 'K' and resid 129 through 134 removed outlier: 3.600A pdb=" N PHE K 134 " --> pdb=" O LYS K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 179 through 183 Processing helix chain 'K' and resid 186 through 203 removed outlier: 3.754A pdb=" N GLN K 198 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG K 199 " --> pdb=" O LYS K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 229 Processing helix chain 'K' and resid 230 through 233 removed outlier: 3.577A pdb=" N LEU K 233 " --> pdb=" O GLN K 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 230 through 233' Processing helix chain 'K' and resid 234 through 302 removed outlier: 3.618A pdb=" N VAL K 238 " --> pdb=" O ASP K 234 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU K 302 " --> pdb=" O GLU K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 363 through 376 Processing helix chain 'K' and resid 382 through 400 removed outlier: 4.044A pdb=" N ALA K 386 " --> pdb=" O ASP K 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER K 387 " --> pdb=" O SER K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 456 Processing helix chain 'L' and resid 53 through 67 Processing helix chain 'M' and resid 131 through 135 Processing helix chain 'M' and resid 156 through 167 Processing helix chain 'M' and resid 179 through 183 Processing helix chain 'M' and resid 186 through 203 removed outlier: 4.024A pdb=" N GLU M 202 " --> pdb=" O GLN M 198 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS M 203 " --> pdb=" O ARG M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 254 Processing helix chain 'M' and resid 258 through 302 removed outlier: 3.685A pdb=" N LEU M 264 " --> pdb=" O GLN M 260 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET M 265 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU M 266 " --> pdb=" O GLN M 262 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU M 302 " --> pdb=" O GLU M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 363 Processing helix chain 'M' and resid 363 through 376 Processing helix chain 'M' and resid 381 through 400 removed outlier: 3.596A pdb=" N THR M 385 " --> pdb=" O ASP M 381 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA M 386 " --> pdb=" O ASP M 382 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER M 387 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 450 through 456 Processing helix chain 'N' and resid 129 through 134 removed outlier: 3.578A pdb=" N PHE N 134 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 167 Processing helix chain 'N' and resid 179 through 183 removed outlier: 3.544A pdb=" N HIS N 182 " --> pdb=" O ASN N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 203 removed outlier: 3.758A pdb=" N GLN N 198 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG N 199 " --> pdb=" O LYS N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 229 Processing helix chain 'N' and resid 230 through 233 removed outlier: 3.565A pdb=" N LEU N 233 " --> pdb=" O GLN N 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 230 through 233' Processing helix chain 'N' and resid 234 through 302 removed outlier: 3.585A pdb=" N VAL N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU N 302 " --> pdb=" O GLU N 298 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 363 Processing helix chain 'N' and resid 363 through 376 Processing helix chain 'N' and resid 382 through 400 removed outlier: 4.041A pdb=" N ALA N 386 " --> pdb=" O ASP N 382 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER N 387 " --> pdb=" O SER N 383 " (cutoff:3.500A) Processing helix chain 'N' and resid 450 through 456 Processing helix chain 'O' and resid 131 through 135 Processing helix chain 'O' and resid 156 through 167 Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 186 through 203 removed outlier: 4.116A pdb=" N GLU O 202 " --> pdb=" O GLN O 198 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS O 203 " --> pdb=" O ARG O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 254 Processing helix chain 'O' and resid 258 through 302 removed outlier: 3.639A pdb=" N LEU O 264 " --> pdb=" O GLN O 260 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET O 265 " --> pdb=" O LEU O 261 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU O 266 " --> pdb=" O GLN O 262 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU O 302 " --> pdb=" O GLU O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 363 Processing helix chain 'O' and resid 363 through 376 Processing helix chain 'O' and resid 382 through 400 removed outlier: 3.875A pdb=" N ALA O 386 " --> pdb=" O ASP O 382 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER O 387 " --> pdb=" O SER O 383 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 456 Processing helix chain 'W' and resid 217 through 229 Processing helix chain 'W' and resid 234 through 302 removed outlier: 3.879A pdb=" N LEU W 302 " --> pdb=" O GLU W 298 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 363 removed outlier: 3.630A pdb=" N HIS W 363 " --> pdb=" O ARG W 359 " (cutoff:3.500A) Processing helix chain 'W' and resid 363 through 376 Processing helix chain 'W' and resid 382 through 400 removed outlier: 3.945A pdb=" N ALA W 386 " --> pdb=" O ASP W 382 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER W 387 " --> pdb=" O SER W 383 " (cutoff:3.500A) Processing helix chain 'W' and resid 450 through 456 Processing helix chain 'X' and resid 217 through 229 Processing helix chain 'X' and resid 234 through 302 removed outlier: 3.777A pdb=" N LEU X 302 " --> pdb=" O GLU X 298 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 363 Processing helix chain 'X' and resid 363 through 376 Processing helix chain 'X' and resid 382 through 400 removed outlier: 3.935A pdb=" N ALA X 386 " --> pdb=" O ASP X 382 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER X 387 " --> pdb=" O SER X 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 456 Processing helix chain 'a' and resid 48 through 62 Processing helix chain 'a' and resid 144 through 158 Processing helix chain 'a' and resid 166 through 176 removed outlier: 3.629A pdb=" N ALA a 170 " --> pdb=" O VAL a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 192 Processing helix chain 'c' and resid 250 through 256 removed outlier: 3.606A pdb=" N SER c 256 " --> pdb=" O ILE c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 381 through 384 Processing helix chain 'c' and resid 985 through 991 Processing helix chain 'c' and resid 1044 through 1062 Processing helix chain 'c' and resid 1069 through 1074 Processing helix chain 'c' and resid 1091 through 1099 removed outlier: 3.893A pdb=" N LEU c1098 " --> pdb=" O ILE c1094 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP c1099 " --> pdb=" O GLU c1095 " (cutoff:3.500A) Processing helix chain 'c' and resid 1101 through 1110 Processing helix chain 'c' and resid 1125 through 1140 removed outlier: 3.825A pdb=" N ILE c1139 " --> pdb=" O GLU c1135 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS c1140 " --> pdb=" O LEU c1136 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 62 Processing helix chain 'd' and resid 144 through 158 Processing helix chain 'd' and resid 166 through 176 Processing helix chain 'd' and resid 176 through 192 Processing helix chain 'f' and resid 250 through 255 Processing helix chain 'f' and resid 381 through 384 Processing helix chain 'f' and resid 985 through 991 Processing helix chain 'f' and resid 1044 through 1059 Processing helix chain 'f' and resid 1069 through 1075 Processing helix chain 'f' and resid 1091 through 1099 Processing helix chain 'f' and resid 1101 through 1110 Processing helix chain 'f' and resid 1125 through 1140 removed outlier: 3.808A pdb=" N ILE f1139 " --> pdb=" O GLU f1135 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS f1140 " --> pdb=" O LEU f1136 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 66 removed outlier: 3.651A pdb=" N LYS h 66 " --> pdb=" O GLN h 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 28 removed outlier: 3.693A pdb=" N ARG b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 34 through 41 removed outlier: 3.814A pdb=" N GLN b 38 " --> pdb=" O THR b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 45 Processing helix chain 'b' and resid 89 through 93 removed outlier: 4.402A pdb=" N ALA b 93 " --> pdb=" O CYS b 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 110 through 124 removed outlier: 4.782A pdb=" N PHE b 121 " --> pdb=" O ARG b 117 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLU b 122 " --> pdb=" O GLY b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 174 Processing helix chain 'b' and resid 216 through 220 Processing helix chain 'b' and resid 263 through 272 removed outlier: 3.883A pdb=" N SER b 269 " --> pdb=" O LEU b 265 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA b 270 " --> pdb=" O LEU b 266 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 311 Processing helix chain 'b' and resid 312 through 327 removed outlier: 4.596A pdb=" N ASP b 324 " --> pdb=" O PHE b 320 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN b 325 " --> pdb=" O GLN b 321 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 353 Processing helix chain 'b' and resid 383 through 391 Processing helix chain 'b' and resid 393 through 399 removed outlier: 3.554A pdb=" N PHE b 397 " --> pdb=" O PHE b 393 " (cutoff:3.500A) Processing helix chain 'b' and resid 415 through 432 Processing helix chain 'b' and resid 436 through 446 Processing helix chain 'b' and resid 458 through 462 removed outlier: 3.561A pdb=" N LEU b 461 " --> pdb=" O SER b 458 " (cutoff:3.500A) Processing helix chain 'e' and resid 17 through 28 removed outlier: 3.686A pdb=" N ARG e 21 " --> pdb=" O ASN e 17 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 41 removed outlier: 3.918A pdb=" N GLN e 38 " --> pdb=" O THR e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 46 Processing helix chain 'e' and resid 89 through 93 removed outlier: 4.360A pdb=" N ALA e 93 " --> pdb=" O CYS e 90 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 124 removed outlier: 4.577A pdb=" N PHE e 121 " --> pdb=" O ARG e 117 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU e 122 " --> pdb=" O GLY e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 174 Processing helix chain 'e' and resid 263 through 272 removed outlier: 3.817A pdb=" N THR e 267 " --> pdb=" O ASP e 263 " (cutoff:3.500A) Processing helix chain 'e' and resid 272 through 282 removed outlier: 3.952A pdb=" N GLN e 276 " --> pdb=" O PHE e 272 " (cutoff:3.500A) Processing helix chain 'e' and resid 293 through 311 Processing helix chain 'e' and resid 312 through 328 removed outlier: 4.455A pdb=" N ASP e 324 " --> pdb=" O PHE e 320 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN e 325 " --> pdb=" O GLN e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 348 through 353 Processing helix chain 'e' and resid 383 through 391 removed outlier: 3.840A pdb=" N GLU e 388 " --> pdb=" O ASP e 384 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU e 391 " --> pdb=" O LEU e 387 " (cutoff:3.500A) Processing helix chain 'e' and resid 393 through 399 removed outlier: 3.613A pdb=" N PHE e 397 " --> pdb=" O PHE e 393 " (cutoff:3.500A) Processing helix chain 'e' and resid 415 through 432 Processing helix chain 'e' and resid 435 through 446 removed outlier: 4.119A pdb=" N GLU e 439 " --> pdb=" O GLY e 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 404 through 412 removed outlier: 6.512A pdb=" N VAL H 727 " --> pdb=" O LEU H 408 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR H 410 " --> pdb=" O ILE H 725 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE H 725 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 424 through 429 removed outlier: 3.721A pdb=" N GLY H 440 " --> pdb=" O LYS H 444 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS H 444 " --> pdb=" O GLY H 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 473 through 478 removed outlier: 4.115A pdb=" N CYS H 475 " --> pdb=" O SER H 489 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR H 494 " --> pdb=" O ASP H 490 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL H 495 " --> pdb=" O VAL H 508 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL H 508 " --> pdb=" O VAL H 495 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU H 497 " --> pdb=" O SER H 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 516 through 521 removed outlier: 3.735A pdb=" N SER H 518 " --> pdb=" O GLY H 532 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS H 537 " --> pdb=" O SER H 533 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER H 542 " --> pdb=" O SER H 548 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER H 548 " --> pdb=" O SER H 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 558 through 563 removed outlier: 6.849A pdb=" N GLY H 574 " --> pdb=" O CYS H 559 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL H 561 " --> pdb=" O ALA H 572 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA H 572 " --> pdb=" O VAL H 561 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N PHE H 563 " --> pdb=" O HIS H 570 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS H 570 " --> pdb=" O PHE H 563 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS H 579 " --> pdb=" O CYS H 575 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 602 through 607 removed outlier: 3.531A pdb=" N LYS H 606 " --> pdb=" O VAL H 614 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN H 621 " --> pdb=" O SER H 617 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN H 626 " --> pdb=" O CYS H 632 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N CYS H 632 " --> pdb=" O ASN H 626 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 648 through 651 Processing sheet with id=AA8, first strand: chain 'I' and resid 404 through 412 removed outlier: 6.506A pdb=" N VAL I 727 " --> pdb=" O LEU I 408 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR I 410 " --> pdb=" O ILE I 725 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE I 725 " --> pdb=" O THR I 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 424 through 429 removed outlier: 3.855A pdb=" N GLY I 440 " --> pdb=" O LYS I 444 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS I 444 " --> pdb=" O GLY I 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 473 through 478 removed outlier: 4.204A pdb=" N CYS I 475 " --> pdb=" O SER I 489 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL I 495 " --> pdb=" O VAL I 508 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL I 508 " --> pdb=" O VAL I 495 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU I 497 " --> pdb=" O SER I 506 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 516 through 521 removed outlier: 3.529A pdb=" N SER I 518 " --> pdb=" O GLY I 532 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS I 537 " --> pdb=" O SER I 533 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER I 542 " --> pdb=" O SER I 548 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER I 548 " --> pdb=" O SER I 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 560 through 563 removed outlier: 4.051A pdb=" N CYS I 560 " --> pdb=" O GLY I 574 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 562 " --> pdb=" O ALA I 572 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 602 through 607 removed outlier: 3.511A pdb=" N TYR I 604 " --> pdb=" O ALA I 616 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS I 606 " --> pdb=" O VAL I 614 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN I 621 " --> pdb=" O SER I 617 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN I 626 " --> pdb=" O CYS I 632 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N CYS I 632 " --> pdb=" O ASN I 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 648 through 651 removed outlier: 3.899A pdb=" N SER I 663 " --> pdb=" O SER I 659 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 154 through 156 Processing sheet with id=AB7, first strand: chain 'K' and resid 404 through 412 removed outlier: 5.307A pdb=" N VAL K 405 " --> pdb=" O VAL K 731 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL K 731 " --> pdb=" O VAL K 405 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU K 729 " --> pdb=" O PRO K 407 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA K 409 " --> pdb=" O VAL K 727 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR K 724 " --> pdb=" O ASN K 720 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 424 through 429 removed outlier: 4.453A pdb=" N LYS K 444 " --> pdb=" O GLY K 440 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 473 through 478 removed outlier: 3.509A pdb=" N CYS K 475 " --> pdb=" O SER K 489 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR K 494 " --> pdb=" O ASP K 490 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL K 495 " --> pdb=" O VAL K 508 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL K 508 " --> pdb=" O VAL K 495 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU K 497 " --> pdb=" O SER K 506 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 516 through 521 removed outlier: 3.888A pdb=" N SER K 518 " --> pdb=" O GLY K 532 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 537 " --> pdb=" O SER K 533 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER K 542 " --> pdb=" O SER K 548 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER K 548 " --> pdb=" O SER K 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 558 through 563 removed outlier: 4.406A pdb=" N CYS K 579 " --> pdb=" O CYS K 575 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 602 through 607 removed outlier: 3.874A pdb=" N TYR K 604 " --> pdb=" O ALA K 616 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN K 626 " --> pdb=" O CYS K 632 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYS K 632 " --> pdb=" O ASN K 626 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 648 through 651 Processing sheet with id=AC5, first strand: chain 'M' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'M' and resid 404 through 412 removed outlier: 5.147A pdb=" N VAL M 405 " --> pdb=" O VAL M 731 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL M 731 " --> pdb=" O VAL M 405 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU M 729 " --> pdb=" O PRO M 407 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA M 409 " --> pdb=" O VAL M 727 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR M 724 " --> pdb=" O ASN M 720 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL M 715 " --> pdb=" O ARG M 706 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 424 through 429 Processing sheet with id=AC8, first strand: chain 'M' and resid 475 through 478 removed outlier: 6.721A pdb=" N VAL M 495 " --> pdb=" O VAL M 508 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL M 508 " --> pdb=" O VAL M 495 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU M 497 " --> pdb=" O SER M 506 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 516 through 521 removed outlier: 3.702A pdb=" N SER M 518 " --> pdb=" O GLY M 532 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS M 537 " --> pdb=" O SER M 533 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 558 through 563 removed outlier: 4.308A pdb=" N CYS M 579 " --> pdb=" O CYS M 575 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 602 through 607 removed outlier: 3.784A pdb=" N TYR M 604 " --> pdb=" O ALA M 616 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN M 621 " --> pdb=" O SER M 617 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 648 through 651 removed outlier: 6.414A pdb=" N TYR M 668 " --> pdb=" O THR M 674 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR M 674 " --> pdb=" O TYR M 668 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 154 through 156 Processing sheet with id=AD5, first strand: chain 'N' and resid 404 through 412 removed outlier: 5.288A pdb=" N VAL N 405 " --> pdb=" O VAL N 731 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL N 731 " --> pdb=" O VAL N 405 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU N 729 " --> pdb=" O PRO N 407 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA N 409 " --> pdb=" O VAL N 727 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR N 724 " --> pdb=" O ASN N 720 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 424 through 429 removed outlier: 3.535A pdb=" N GLY N 440 " --> pdb=" O LYS N 444 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS N 444 " --> pdb=" O GLY N 440 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 473 through 478 removed outlier: 6.825A pdb=" N VAL N 495 " --> pdb=" O VAL N 508 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL N 508 " --> pdb=" O VAL N 495 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU N 497 " --> pdb=" O SER N 506 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 516 through 521 removed outlier: 3.547A pdb=" N SER N 518 " --> pdb=" O GLY N 532 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS N 537 " --> pdb=" O SER N 533 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER N 542 " --> pdb=" O SER N 548 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER N 548 " --> pdb=" O SER N 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 558 through 563 removed outlier: 4.371A pdb=" N CYS N 579 " --> pdb=" O CYS N 575 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 602 through 607 removed outlier: 3.888A pdb=" N TYR N 604 " --> pdb=" O ALA N 616 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN N 626 " --> pdb=" O CYS N 632 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS N 632 " --> pdb=" O ASN N 626 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 648 through 651 Processing sheet with id=AE3, first strand: chain 'O' and resid 154 through 155 removed outlier: 3.546A pdb=" N TYR O 147 " --> pdb=" O PHE O 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 404 through 412 removed outlier: 5.151A pdb=" N VAL O 405 " --> pdb=" O VAL O 731 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL O 731 " --> pdb=" O VAL O 405 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU O 729 " --> pdb=" O PRO O 407 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 409 " --> pdb=" O VAL O 727 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR O 724 " --> pdb=" O ASN O 720 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL O 715 " --> pdb=" O ARG O 706 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'O' and resid 424 through 429 Processing sheet with id=AE6, first strand: chain 'O' and resid 475 through 478 removed outlier: 6.713A pdb=" N VAL O 495 " --> pdb=" O VAL O 508 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL O 508 " --> pdb=" O VAL O 495 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU O 497 " --> pdb=" O SER O 506 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 516 through 521 removed outlier: 3.700A pdb=" N SER O 518 " --> pdb=" O GLY O 532 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS O 537 " --> pdb=" O SER O 533 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER O 542 " --> pdb=" O SER O 548 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER O 548 " --> pdb=" O SER O 542 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 558 through 563 removed outlier: 4.319A pdb=" N CYS O 579 " --> pdb=" O CYS O 575 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 602 through 607 removed outlier: 3.797A pdb=" N TYR O 604 " --> pdb=" O ALA O 616 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN O 621 " --> pdb=" O SER O 617 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 648 through 651 removed outlier: 6.412A pdb=" N TYR O 668 " --> pdb=" O THR O 674 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR O 674 " --> pdb=" O TYR O 668 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 404 through 412 removed outlier: 6.595A pdb=" N VAL W 727 " --> pdb=" O LEU W 408 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR W 410 " --> pdb=" O ILE W 725 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE W 725 " --> pdb=" O THR W 410 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 426 through 429 Processing sheet with id=AF4, first strand: chain 'W' and resid 475 through 478 removed outlier: 3.935A pdb=" N CYS W 475 " --> pdb=" O SER W 489 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASP W 499 " --> pdb=" O ARG W 505 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG W 505 " --> pdb=" O ASP W 499 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 516 through 521 removed outlier: 3.863A pdb=" N LYS W 537 " --> pdb=" O SER W 533 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER W 542 " --> pdb=" O SER W 548 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER W 548 " --> pdb=" O SER W 542 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 560 through 563 removed outlier: 3.957A pdb=" N CYS W 560 " --> pdb=" O GLY W 574 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 602 through 607 removed outlier: 3.656A pdb=" N TYR W 604 " --> pdb=" O ALA W 616 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN W 621 " --> pdb=" O SER W 617 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN W 626 " --> pdb=" O CYS W 632 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N CYS W 632 " --> pdb=" O ASN W 626 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 648 through 651 Processing sheet with id=AF9, first strand: chain 'X' and resid 404 through 412 removed outlier: 6.616A pdb=" N VAL X 727 " --> pdb=" O LEU X 408 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR X 410 " --> pdb=" O ILE X 725 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE X 725 " --> pdb=" O THR X 410 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 426 through 429 Processing sheet with id=AG2, first strand: chain 'X' and resid 473 through 478 removed outlier: 3.855A pdb=" N CYS X 475 " --> pdb=" O SER X 489 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR X 494 " --> pdb=" O ASP X 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP X 499 " --> pdb=" O ARG X 505 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG X 505 " --> pdb=" O ASP X 499 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 516 through 521 removed outlier: 3.852A pdb=" N LYS X 537 " --> pdb=" O SER X 533 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER X 542 " --> pdb=" O SER X 548 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER X 548 " --> pdb=" O SER X 542 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 560 through 563 removed outlier: 4.133A pdb=" N CYS X 560 " --> pdb=" O GLY X 574 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 602 through 607 removed outlier: 3.644A pdb=" N TYR X 604 " --> pdb=" O ALA X 616 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN X 621 " --> pdb=" O SER X 617 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN X 626 " --> pdb=" O CYS X 632 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N CYS X 632 " --> pdb=" O ASN X 626 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 648 through 651 Processing sheet with id=AG7, first strand: chain 'a' and resid 67 through 71 removed outlier: 3.768A pdb=" N ILE a 100 " --> pdb=" O TRP a 79 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'c' and resid 1004 through 1009 removed outlier: 4.619A pdb=" N VAL c1006 " --> pdb=" O GLY c1031 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN c1025 " --> pdb=" O SER c1042 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER c1027 " --> pdb=" O VAL c1040 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL c1040 " --> pdb=" O SER c1027 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU c1029 " --> pdb=" O GLY c1038 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY c1038 " --> pdb=" O LEU c1029 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE c1037 " --> pdb=" O ALA c 9 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR c 3 " --> pdb=" O LEU c1043 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASN c 4 " --> pdb=" O ILE c1089 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 17 through 21 removed outlier: 6.727A pdb=" N LEU c 39 " --> pdb=" O GLU c 54 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU c 54 " --> pdb=" O LEU c 39 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE c 41 " --> pdb=" O VAL c 52 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'c' and resid 61 through 67 removed outlier: 3.584A pdb=" N VAL c 63 " --> pdb=" O LEU c 80 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN c 85 " --> pdb=" O THR c 81 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA c 86 " --> pdb=" O HIS c 105 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS c 105 " --> pdb=" O ALA c 86 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE c 88 " --> pdb=" O ARG c 103 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 121 through 124 Processing sheet with id=AH3, first strand: chain 'c' and resid 163 through 169 removed outlier: 5.206A pdb=" N VAL c 164 " --> pdb=" O GLN c 183 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN c 183 " --> pdb=" O VAL c 164 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 163 through 169 removed outlier: 5.206A pdb=" N VAL c 164 " --> pdb=" O GLN c 183 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN c 183 " --> pdb=" O VAL c 164 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG c 188 " --> pdb=" O VAL c 212 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'c' and resid 216 through 221 removed outlier: 6.583A pdb=" N ILE c 232 " --> pdb=" O SER c 217 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL c 219 " --> pdb=" O ILE c 230 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE c 230 " --> pdb=" O VAL c 219 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'c' and resid 258 through 263 removed outlier: 4.336A pdb=" N ARG c 279 " --> pdb=" O ASP c 275 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU c 280 " --> pdb=" O LEU c 305 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP c 299 " --> pdb=" O GLU c 286 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU c 288 " --> pdb=" O LEU c 297 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU c 297 " --> pdb=" O GLU c 288 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'c' and resid 316 through 318 removed outlier: 5.291A pdb=" N TYR c 316 " --> pdb=" O PHE c 323 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE c 323 " --> pdb=" O TYR c 316 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP c 318 " --> pdb=" O VAL c 321 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER c 331 " --> pdb=" O THR c 352 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR c 352 " --> pdb=" O SER c 331 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU c 333 " --> pdb=" O MET c 350 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'c' and resid 359 through 365 removed outlier: 4.306A pdb=" N ASP c 361 " --> pdb=" O CYS c 378 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 720 through 727 removed outlier: 6.689A pdb=" N SER c 738 " --> pdb=" O PRO c 721 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS c 723 " --> pdb=" O LEU c 736 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'c' and resid 720 through 727 removed outlier: 6.689A pdb=" N SER c 738 " --> pdb=" O PRO c 721 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS c 723 " --> pdb=" O LEU c 736 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASP c 795 " --> pdb=" O VAL c 801 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL c 801 " --> pdb=" O ASP c 795 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER c 764 " --> pdb=" O GLN c 806 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'c' and resid 811 through 819 removed outlier: 6.866A pdb=" N GLY c 832 " --> pdb=" O LEU c 814 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU c 816 " --> pdb=" O ILE c 830 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE c 830 " --> pdb=" O LEU c 816 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER c 818 " --> pdb=" O TYR c 828 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR c 828 " --> pdb=" O SER c 818 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN c 852 " --> pdb=" O THR c 860 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR c 860 " --> pdb=" O GLN c 852 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER c 854 " --> pdb=" O LEU c 858 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU c 858 " --> pdb=" O SER c 854 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'c' and resid 870 through 876 removed outlier: 6.291A pdb=" N SER c 883 " --> pdb=" O TYR c 871 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET c 873 " --> pdb=" O LEU c 881 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU c 881 " --> pdb=" O MET c 873 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU c 875 " --> pdb=" O LYS c 879 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS c 879 " --> pdb=" O GLU c 875 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLU c 892 " --> pdb=" O THR c 901 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR c 901 " --> pdb=" O GLU c 892 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'c' and resid 913 through 917 removed outlier: 3.787A pdb=" N TYR c 913 " --> pdb=" O GLY c 924 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL c 930 " --> pdb=" O ARG c 947 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ARG c 947 " --> pdb=" O VAL c 930 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU c 932 " --> pdb=" O ILE c 945 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'c' and resid 956 through 959 removed outlier: 3.876A pdb=" N ALA c 956 " --> pdb=" O ALA c 968 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 1076 through 1077 Processing sheet with id=AI7, first strand: chain 'c' and resid 1113 through 1114 Processing sheet with id=AI8, first strand: chain 'd' and resid 67 through 71 removed outlier: 3.504A pdb=" N ILE d 100 " --> pdb=" O TRP d 79 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'f' and resid 1004 through 1009 removed outlier: 6.631A pdb=" N GLY f1031 " --> pdb=" O ASN f1005 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE f1007 " --> pdb=" O LEU f1029 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU f1029 " --> pdb=" O PHE f1007 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N HIS f1009 " --> pdb=" O SER f1027 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER f1027 " --> pdb=" O HIS f1009 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN f1025 " --> pdb=" O SER f1042 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER f1027 " --> pdb=" O VAL f1040 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL f1040 " --> pdb=" O SER f1027 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU f1029 " --> pdb=" O GLY f1038 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY f1038 " --> pdb=" O LEU f1029 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE f1037 " --> pdb=" O ALA f 9 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR f 3 " --> pdb=" O LEU f1043 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'f' and resid 17 through 21 removed outlier: 6.733A pdb=" N LEU f 39 " --> pdb=" O GLU f 54 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU f 54 " --> pdb=" O LEU f 39 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE f 41 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'f' and resid 61 through 67 removed outlier: 6.337A pdb=" N LEU f 80 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N MET f 64 " --> pdb=" O PHE f 78 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE f 78 " --> pdb=" O MET f 64 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU f 66 " --> pdb=" O LEU f 76 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU f 76 " --> pdb=" O LEU f 66 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN f 85 " --> pdb=" O THR f 81 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA f 86 " --> pdb=" O HIS f 105 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N HIS f 105 " --> pdb=" O ALA f 86 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE f 88 " --> pdb=" O ARG f 103 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'f' and resid 93 through 94 Processing sheet with id=AJ4, first strand: chain 'f' and resid 121 through 124 Processing sheet with id=AJ5, first strand: chain 'f' and resid 164 through 170 removed outlier: 5.084A pdb=" N VAL f 164 " --> pdb=" O GLN f 183 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN f 183 " --> pdb=" O VAL f 164 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR f 177 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'f' and resid 164 through 170 removed outlier: 5.084A pdb=" N VAL f 164 " --> pdb=" O GLN f 183 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN f 183 " --> pdb=" O VAL f 164 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR f 177 " --> pdb=" O LEU f 170 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG f 188 " --> pdb=" O VAL f 212 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'f' and resid 216 through 221 Processing sheet with id=AJ8, first strand: chain 'f' and resid 258 through 263 removed outlier: 4.308A pdb=" N ARG f 279 " --> pdb=" O ASP f 275 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU f 280 " --> pdb=" O LEU f 305 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP f 299 " --> pdb=" O GLU f 286 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU f 288 " --> pdb=" O LEU f 297 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU f 297 " --> pdb=" O GLU f 288 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'f' and resid 313 through 316 removed outlier: 3.770A pdb=" N CYS f 313 " --> pdb=" O GLY f 325 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER f 331 " --> pdb=" O THR f 352 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR f 352 " --> pdb=" O SER f 331 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU f 333 " --> pdb=" O MET f 350 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'f' and resid 359 through 365 removed outlier: 4.308A pdb=" N ASP f 361 " --> pdb=" O CYS f 378 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'f' and resid 720 through 727 removed outlier: 6.694A pdb=" N SER f 738 " --> pdb=" O PRO f 721 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS f 723 " --> pdb=" O LEU f 736 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'f' and resid 720 through 727 removed outlier: 6.694A pdb=" N SER f 738 " --> pdb=" O PRO f 721 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS f 723 " --> pdb=" O LEU f 736 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP f 795 " --> pdb=" O VAL f 801 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL f 801 " --> pdb=" O ASP f 795 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER f 764 " --> pdb=" O GLN f 806 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'f' and resid 811 through 819 removed outlier: 6.825A pdb=" N GLY f 832 " --> pdb=" O LEU f 814 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU f 816 " --> pdb=" O ILE f 830 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE f 830 " --> pdb=" O LEU f 816 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER f 818 " --> pdb=" O TYR f 828 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR f 828 " --> pdb=" O SER f 818 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN f 845 " --> pdb=" O MET f 835 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN f 852 " --> pdb=" O THR f 860 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR f 860 " --> pdb=" O GLN f 852 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER f 854 " --> pdb=" O LEU f 858 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU f 858 " --> pdb=" O SER f 854 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'f' and resid 870 through 876 removed outlier: 6.159A pdb=" N SER f 883 " --> pdb=" O TYR f 871 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET f 873 " --> pdb=" O LEU f 881 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU f 881 " --> pdb=" O MET f 873 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU f 875 " --> pdb=" O LYS f 879 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS f 879 " --> pdb=" O GLU f 875 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL f 888 " --> pdb=" O ASN f 904 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN f 904 " --> pdb=" O VAL f 888 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU f 890 " --> pdb=" O GLU f 902 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'f' and resid 913 through 917 removed outlier: 3.839A pdb=" N TYR f 913 " --> pdb=" O GLY f 924 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL f 930 " --> pdb=" O ARG f 947 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ARG f 947 " --> pdb=" O VAL f 930 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU f 932 " --> pdb=" O ILE f 945 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'f' and resid 956 through 959 removed outlier: 3.789A pdb=" N ALA f 956 " --> pdb=" O ALA f 968 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN f 978 " --> pdb=" O GLU f 994 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU f 994 " --> pdb=" O GLN f 978 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'f' and resid 1076 through 1077 Processing sheet with id=AK9, first strand: chain 'f' and resid 1113 through 1115 Processing sheet with id=AL1, first strand: chain 'b' and resid 51 through 52 removed outlier: 6.637A pdb=" N THR b 51 " --> pdb=" O LEU b 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL1 Processing sheet with id=AL2, first strand: chain 'b' and resid 60 through 65 removed outlier: 5.336A pdb=" N LEU b 62 " --> pdb=" O PHE b 75 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE b 75 " --> pdb=" O LEU b 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS b 64 " --> pdb=" O ILE b 73 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU b 86 " --> pdb=" O LEU b 127 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU b 127 " --> pdb=" O GLU b 86 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'b' and resid 139 through 140 Processing sheet with id=AL4, first strand: chain 'b' and resid 139 through 140 removed outlier: 6.239A pdb=" N ASP b 197 " --> pdb=" O LEU b 203 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU b 203 " --> pdb=" O ASP b 197 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'b' and resid 222 through 225 removed outlier: 6.481A pdb=" N ILE b 239 " --> pdb=" O THR b 255 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR b 255 " --> pdb=" O ILE b 239 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL b 241 " --> pdb=" O VAL b 253 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'b' and resid 330 through 335 removed outlier: 6.718A pdb=" N LYS b 345 " --> pdb=" O TRP b 332 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET b 334 " --> pdb=" O PHE b 343 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE b 343 " --> pdb=" O MET b 334 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'b' and resid 487 through 488 Processing sheet with id=AL8, first strand: chain 'b' and resid 517 through 521 Processing sheet with id=AL9, first strand: chain 'e' and resid 104 through 105 removed outlier: 6.774A pdb=" N THR e 51 " --> pdb=" O LEU e 105 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'e' and resid 60 through 65 removed outlier: 5.346A pdb=" N LEU e 62 " --> pdb=" O PHE e 75 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE e 75 " --> pdb=" O LEU e 62 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS e 64 " --> pdb=" O ILE e 73 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER e 81 " --> pdb=" O SER e 76 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU e 86 " --> pdb=" O LEU e 127 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU e 127 " --> pdb=" O GLU e 86 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'e' and resid 139 through 140 Processing sheet with id=AM3, first strand: chain 'e' and resid 139 through 140 removed outlier: 6.263A pdb=" N ASP e 197 " --> pdb=" O LEU e 203 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU e 203 " --> pdb=" O ASP e 197 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'e' and resid 222 through 225 removed outlier: 6.451A pdb=" N ILE e 239 " --> pdb=" O THR e 255 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR e 255 " --> pdb=" O ILE e 239 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL e 241 " --> pdb=" O VAL e 253 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR e 249 " --> pdb=" O THR e 245 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'e' and resid 330 through 338 removed outlier: 3.590A pdb=" N LYS e 345 " --> pdb=" O TRP e 332 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET e 334 " --> pdb=" O PHE e 343 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE e 343 " --> pdb=" O MET e 334 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LEU e 336 " --> pdb=" O HIS e 341 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS e 341 " --> pdb=" O LEU e 336 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN e 369 " --> pdb=" O VAL e 375 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL e 375 " --> pdb=" O ASN e 369 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'e' and resid 466 through 467 removed outlier: 3.912A pdb=" N TYR e 490 " --> pdb=" O SER e 467 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA e 491 " --> pdb=" O LEU e 497 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU e 497 " --> pdb=" O ALA e 491 " (cutoff:3.500A) 2513 hydrogen bonds defined for protein. 7068 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: 12.58 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13935 1.34 - 1.46: 4180 1.46 - 1.57: 17791 1.57 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 35909 Sorted by residual: bond pdb=" CB ARG e 298 " pdb=" CG ARG e 298 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" N PRO c 754 " pdb=" CD PRO c 754 " ideal model delta sigma weight residual 1.473 1.487 -0.014 1.40e-02 5.10e+03 1.06e+00 bond pdb=" C ASN c 885 " pdb=" O ASN c 885 " ideal model delta sigma weight residual 1.243 1.235 0.009 9.50e-03 1.11e+04 8.17e-01 bond pdb=" CA VAL N 558 " pdb=" CB VAL N 558 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 7.01e-01 bond pdb=" CA VAL M 558 " pdb=" CB VAL M 558 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.05e-02 9.07e+03 6.83e-01 ... (remaining 35904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 49294 1.47 - 2.94: 572 2.94 - 4.41: 146 4.41 - 5.87: 2 5.87 - 7.34: 2 Bond angle restraints: 50016 Sorted by residual: angle pdb=" C ASN c 885 " pdb=" CA ASN c 885 " pdb=" CB ASN c 885 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" N THR e 372 " pdb=" CA THR e 372 " pdb=" C THR e 372 " ideal model delta sigma weight residual 114.09 106.75 7.34 1.55e+00 4.16e-01 2.24e+01 angle pdb=" CA ASN c 885 " pdb=" C ASN c 885 " pdb=" N SER c 886 " ideal model delta sigma weight residual 119.98 116.88 3.10 8.50e-01 1.38e+00 1.33e+01 angle pdb=" CA THR e 372 " pdb=" C THR e 372 " pdb=" N THR e 373 " ideal model delta sigma weight residual 119.07 115.58 3.49 1.23e+00 6.61e-01 8.03e+00 angle pdb=" N ILE M 138 " pdb=" CA ILE M 138 " pdb=" C ILE M 138 " ideal model delta sigma weight residual 111.67 109.27 2.40 9.50e-01 1.11e+00 6.40e+00 ... (remaining 50011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 20544 15.11 - 30.23: 346 30.23 - 45.34: 189 45.34 - 60.46: 6 60.46 - 75.57: 2 Dihedral angle restraints: 21087 sinusoidal: 1063 harmonic: 20024 Sorted by residual: dihedral pdb=" CA GLN h 45 " pdb=" CB GLN h 45 " pdb=" CG GLN h 45 " pdb=" CD GLN h 45 " ideal model delta sinusoidal sigma weight residual 60.00 106.44 -46.44 3 1.50e+01 4.44e-03 8.34e+00 dihedral pdb=" CA ASP H 231 " pdb=" C ASP H 231 " pdb=" N ASN H 232 " pdb=" CA ASN H 232 " ideal model delta harmonic sigma weight residual 180.00 165.57 14.43 0 5.00e+00 4.00e-02 8.33e+00 dihedral pdb=" CA ILE h 47 " pdb=" CB ILE h 47 " pdb=" CG1 ILE h 47 " pdb=" CD1 ILE h 47 " ideal model delta sinusoidal sigma weight residual 60.00 104.37 -44.37 3 1.50e+01 4.44e-03 7.98e+00 ... (remaining 21084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3970 0.028 - 0.055: 1584 0.055 - 0.083: 416 0.083 - 0.110: 498 0.110 - 0.138: 139 Chirality restraints: 6607 Sorted by residual: chirality pdb=" CA ILE h 46 " pdb=" N ILE h 46 " pdb=" C ILE h 46 " pdb=" CB ILE h 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE W 427 " pdb=" N ILE W 427 " pdb=" C ILE W 427 " pdb=" CB ILE W 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE H 427 " pdb=" N ILE H 427 " pdb=" C ILE H 427 " pdb=" CB ILE H 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 6604 not shown) Planarity restraints: 7196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP f 125 " -0.023 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO f 126 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO f 126 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO f 126 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR c 837 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO c 838 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO c 838 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO c 838 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE c 143 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO c 144 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO c 144 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO c 144 " -0.018 5.00e-02 4.00e+02 ... (remaining 7193 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10221 2.80 - 3.33: 31008 3.33 - 3.85: 53622 3.85 - 4.38: 48134 4.38 - 4.90: 93242 Nonbonded interactions: 236227 Sorted by model distance: nonbonded pdb=" O ASN N 484 " pdb=" N GLY N 500 " model vdw 2.280 3.120 nonbonded pdb=" N SER M 474 " pdb=" O SER M 489 " model vdw 2.285 3.120 nonbonded pdb=" OH TYR d 191 " pdb=" OD1 ASP e 264 " model vdw 2.288 3.040 nonbonded pdb=" N SER O 474 " pdb=" O SER O 489 " model vdw 2.289 3.120 nonbonded pdb=" O ASN K 484 " pdb=" N GLY K 500 " model vdw 2.292 3.120 ... (remaining 236222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 216 through 217 or resid 221 or resid 223 through 224 or r \ esid 231 through 232 or resid 234 through 235 or resid 237 through 254 or resid \ 257 through 413 or (resid 423 through 468 and (name N or name CA or name C or na \ me O or name CB )) or resid 473 through 731)) selection = (chain 'I' and (resid 216 through 217 or resid 221 or resid 223 through 224 or r \ esid 231 through 232 or resid 234 through 235 or resid 237 through 254 or resid \ 257 through 405 or (resid 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 413 or (resid 423 through 439 and (name N or name CA \ or name C or name O or name CB )) or (resid 440 through 468 and (name N or name \ CA or name C or name O or name CB )) or (resid 473 through 492 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 493 through 502 and (name N o \ r name CA or name C or name O or name CB )) or (resid 503 through 525 and (name \ N or name CA or name C or name O or name CB )) or resid 526 through 644 or (resi \ d 645 through 646 and (name N or name CA or name C or name O or name CB )) or (r \ esid 647 through 657 and (name N or name CA or name C or name O or name CB )) or \ (resid 658 through 669 and (name N or name CA or name C or name O or name CB )) \ or (resid 670 through 708 and (name N or name CA or name C or name O or name CB \ )) or resid 709 through 731)) selection = (chain 'M' and (resid 152 through 153 or resid 160 or resid 162 or resid 166 or \ resid 178 through 179 or resid 181 or resid 188 or resid 190 or resid 238 throug \ h 284 or resid 347 through 480 or (resid 481 through 492 and (name N or name CA \ or name C or name O or name CB )) or resid 493 through 679 or resid 700 through \ 731)) selection = (chain 'O' and (resid 152 through 153 or resid 160 or resid 162 or resid 166 or \ resid 178 through 179 or resid 181 or resid 188 or resid 190 or resid 238 throug \ h 284 or resid 347 through 679 or resid 700 through 731)) selection = (chain 'W' and (resid 216 through 217 or resid 221 or resid 223 through 224 or r \ esid 231 through 232 or resid 234 through 235 or resid 237 through 254 or resid \ 257 through 284 or resid 347 through 413 or resid 423 through 468 or resid 473 t \ hrough 731)) selection = (chain 'X' and (resid 216 through 217 or resid 221 or resid 223 through 224 or r \ esid 231 through 232 or resid 234 through 235 or resid 237 through 254 or resid \ 257 through 284 or resid 347 through 413 or resid 423 through 468 or resid 473 t \ hrough 731)) } ncs_group { reference = (chain 'K' and (resid 128 through 516 or (resid 517 through 525 and (name N or n \ ame CA or name C or name O or name CB )) or resid 526 through 606 or (resid 607 \ through 609 and (name N or name CA or name C or name O or name CB )) or resid 61 \ 0 through 731)) selection = (chain 'N' and (resid 128 through 511 or (resid 512 through 525 and (name N or n \ ame CA or name C or name O or name CB )) or resid 526 through 585 or (resid 586 \ through 590 and (name N or name CA or name C or name O or name CB )) or resid 59 \ 1 through 731)) } ncs_group { reference = chain 'L' selection = (chain 'h' and ((resid 2 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 or (resid 10 through 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 18 or (resid 19 through 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 or (resid 36 and (na \ me N or name CA or name C or name O or name CB )) or resid 37 or (resid 38 throu \ gh 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ esid 43 through 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 49 or (resid 50 through 53 and (name N or name CA or name C or n \ ame O or name CB )) or resid 54 or (resid 55 and (name N or name CA or name C or \ name O or name CB )) or resid 56 through 57 or (resid 58 and (name N or name CA \ or name C or name O or name CB )) or resid 59 through 60 or (resid 61 through 6 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 63 or (resid \ 64 through 67 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'a' and ((resid 47 through 62 and (name N or name CA or name C or name O \ or name CB )) or resid 63 through 160 or (resid 161 through 166 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 167 through 186 and (name N o \ r name CA or name C or name O or name CB )) or resid 187 through 189 or (resid 1 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 191 through \ 193)) selection = (chain 'd' and (resid 47 through 75 or (resid 76 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 193)) } ncs_group { reference = (chain 'b' and (resid 10 through 13 or (resid 14 through 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 44 or (resid 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 48 or (res \ id 49 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 99 or (resid 100 through 101 and (name N or name CA or name C or n \ ame O or name CB )) or resid 102 through 219 or resid 221 through 345 or (resid \ 346 through 358 and (name N or name CA or name C or name O or name CB )) or resi \ d 359 through 444 or (resid 445 and (name N or name CA or name C or name O or na \ me CB )) or resid 446 through 462 or (resid 463 through 465 and (name N or name \ CA or name C or name O or name CB )) or resid 466 through 484 or (resid 485 and \ (name N or name CA or name C or name O or name CB )) or resid 486 through 489 or \ (resid 490 through 491 and (name N or name CA or name C or name O or name CB )) \ or resid 492 through 519 or (resid 520 through 523 and (name N or name CA or na \ me C or name O or name CB )) or resid 524 through 527 or (resid 528 through 548 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'e' and (resid 10 through 12 or (resid 13 through 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 38 or (resid 39 and (na \ me N or name CA or name C or name O or name CB )) or resid 40 through 182 or (re \ sid 183 and (name N or name CA or name C or name O or name CB )) or resid 184 th \ rough 214 or (resid 215 through 217 and (name N or name CA or name C or name O o \ r name CB )) or resid 218 through 236 or (resid 237 through 245 and (name N or n \ ame CA or name C or name O or name CB )) or resid 246 through 258 or (resid 259 \ through 260 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 1 through 263 or (resid 264 through 272 and (name N or name CA or name C or name \ O or name CB )) or resid 273 or resid 290 through 317 or (resid 318 through 331 \ and (name N or name CA or name C or name O or name CB )) or resid 332 through 3 \ 38 or (resid 339 through 340 and (name N or name CA or name C or name O or name \ CB )) or resid 341 through 388 or (resid 389 and (name N or name CA or name C or \ name O or name CB )) or resid 390 through 393 or (resid 394 through 396 and (na \ me N or name CA or name C or name O or name CB )) or resid 397 through 401 or (r \ esid 402 through 407 and (name N or name CA or name C or name O or name CB )) or \ resid 408 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 through 450 or (resid 451 through 452 and (name N or \ name CA or name C or name O or name CB )) or resid 453 through 467 or (resid 468 \ through 478 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 79 through 497 or (resid 498 through 503 and (name N or name CA or name C or nam \ e O or name CB )) or resid 504 through 548)) } ncs_group { reference = (chain 'c' and ((resid 1 through 16 and (name N or name CA or name C or name O o \ r name CB )) or (resid 17 through 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 through 1000 or resid 1002 through 1073 or (resid 1074 \ through 1083 and (name N or name CA or name C or name O or name CB )) or resid \ 1084 through 1140)) selection = (chain 'f' and (resid 1 through 912 or (resid 913 through 917 and (name N or nam \ e CA or name C or name O or name CB )) or resid 918 through 996 or (resid 997 an \ d (name N or name CA or name C or name O or name CB )) or resid 998 through 1140 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 47.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 42.420 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5675 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 0.040 35909 Z= 0.091 Angle : 0.427 7.342 50016 Z= 0.240 Chirality : 0.043 0.138 6607 Planarity : 0.003 0.036 7196 Dihedral : 7.872 75.572 7953 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.94 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.11), residues: 6807 helix: 3.83 (0.12), residues: 1649 sheet: 0.79 (0.12), residues: 2143 loop : 0.02 (0.12), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 190 TYR 0.014 0.000 TYR e 468 PHE 0.012 0.001 PHE e 364 TRP 0.013 0.001 TRP h 63 HIS 0.009 0.001 HIS b 35 Details of bonding type rmsd covalent geometry : bond 0.00197 (35909) covalent geometry : angle 0.42676 (50016) hydrogen bonds : bond 0.13912 ( 2474) hydrogen bonds : angle 5.08486 ( 7068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: e 364 PHE cc_start: 0.8792 (p90) cc_final: 0.8569 (m-80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1607 time to fit residues: 45.5405 Evaluate side-chains 141 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 40.0000 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 597 optimal weight: 50.0000 overall best weight: 11.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 GLN ** b 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 335 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.042019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031675 restraints weight = 396655.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031675 restraints weight = 424876.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031675 restraints weight = 424876.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031675 restraints weight = 424876.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.031675 restraints weight = 424876.830| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.166 35909 Z= 0.427 Angle : 0.810 10.410 50016 Z= 0.500 Chirality : 0.047 0.230 6607 Planarity : 0.006 0.066 7196 Dihedral : 6.314 27.383 6913 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 2.26 % Allowed : 9.27 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.10), residues: 6807 helix: 0.38 (0.11), residues: 1708 sheet: -0.35 (0.12), residues: 2016 loop : -1.14 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG b 25 TYR 0.031 0.002 TYR b 368 PHE 0.032 0.003 PHE K 607 TRP 0.047 0.004 TRP d 187 HIS 0.010 0.003 HIS N 512 Details of bonding type rmsd covalent geometry : bond 0.00683 (35909) covalent geometry : angle 0.81010 (50016) hydrogen bonds : bond 0.06636 ( 2474) hydrogen bonds : angle 7.07638 ( 7068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.266 Fit side-chains REVERT: e 368 TYR cc_start: 0.1555 (OUTLIER) cc_final: 0.1355 (p90) outliers start: 9 outliers final: 2 residues processed: 143 average time/residue: 0.1490 time to fit residues: 41.2063 Evaluate side-chains 134 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 557 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 585 optimal weight: 20.0000 chunk 500 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 627 optimal weight: 6.9990 chunk 389 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 HIS ** b 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 416 ASN b 544 HIS ** e 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.039793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039788 restraints weight = 375261.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039781 restraints weight = 403.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039780 restraints weight = 261.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039778 restraints weight = 201.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.039778 restraints weight = 207.566| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.155 35909 Z= 0.484 Angle : 0.921 16.986 50016 Z= 0.568 Chirality : 0.049 0.338 6607 Planarity : 0.008 0.166 7196 Dihedral : 8.090 44.114 6913 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.11 % Favored : 87.76 % Rotamer: Outliers : 1.50 % Allowed : 9.77 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.09), residues: 6807 helix: -1.67 (0.11), residues: 1636 sheet: -1.52 (0.12), residues: 1700 loop : -2.36 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG e 12 TYR 0.056 0.003 TYR e 225 PHE 0.043 0.003 PHE b 365 TRP 0.048 0.004 TRP b 332 HIS 0.023 0.005 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00768 (35909) covalent geometry : angle 0.92137 (50016) hydrogen bonds : bond 0.08385 ( 2474) hydrogen bonds : angle 9.10034 ( 7068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 1.291 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 132 average time/residue: 0.1524 time to fit residues: 38.9380 Evaluate side-chains 124 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 335 optimal weight: 0.0970 chunk 635 optimal weight: 7.9990 chunk 325 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 545 optimal weight: 20.0000 chunk 179 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 371 optimal weight: 5.9990 chunk 399 optimal weight: 40.0000 chunk 93 optimal weight: 7.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 237 GLN e 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = 367881.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = 368307.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = 6.654 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = 5.051 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040815 restraints weight = 5.051 | |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35909 Z= 0.215 Angle : 0.582 11.143 50016 Z= 0.345 Chirality : 0.044 0.139 6607 Planarity : 0.005 0.067 7196 Dihedral : 5.980 28.423 6913 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.89 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.10), residues: 6807 helix: -0.35 (0.12), residues: 1655 sheet: -1.61 (0.12), residues: 1826 loop : -2.08 (0.11), residues: 3326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 57 TYR 0.021 0.001 TYR b 455 PHE 0.020 0.001 PHE e 393 TRP 0.014 0.001 TRP b 332 HIS 0.007 0.002 HIS N 512 Details of bonding type rmsd covalent geometry : bond 0.00359 (35909) covalent geometry : angle 0.58198 (50016) hydrogen bonds : bond 0.04900 ( 2474) hydrogen bonds : angle 7.23685 ( 7068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.399 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1600 time to fit residues: 41.6341 Evaluate side-chains 126 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 192 optimal weight: 0.7980 chunk 145 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 474 optimal weight: 20.0000 chunk 461 optimal weight: 30.0000 chunk 209 optimal weight: 3.9990 chunk 165 optimal weight: 50.0000 chunk 307 optimal weight: 0.0030 chunk 600 optimal weight: 30.0000 chunk 180 optimal weight: 30.0000 overall best weight: 6.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.040706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040698 restraints weight = 367022.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040688 restraints weight = 381.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040689 restraints weight = 239.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040688 restraints weight = 195.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040688 restraints weight = 191.396| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5139 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 35909 Z= 0.229 Angle : 0.574 11.492 50016 Z= 0.339 Chirality : 0.044 0.164 6607 Planarity : 0.005 0.064 7196 Dihedral : 5.503 32.791 6913 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.96 % Favored : 89.03 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.10), residues: 6807 helix: 0.30 (0.12), residues: 1652 sheet: -1.71 (0.12), residues: 1831 loop : -2.10 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 190 TYR 0.034 0.002 TYR b 455 PHE 0.033 0.001 PHE b 543 TRP 0.033 0.002 TRP e 332 HIS 0.007 0.002 HIS b 37 Details of bonding type rmsd covalent geometry : bond 0.00383 (35909) covalent geometry : angle 0.57428 (50016) hydrogen bonds : bond 0.04730 ( 2474) hydrogen bonds : angle 6.81841 ( 7068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.477 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1647 time to fit residues: 41.9494 Evaluate side-chains 126 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 547 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 528 optimal weight: 40.0000 chunk 419 optimal weight: 10.0000 chunk 80 optimal weight: 0.0980 chunk 261 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 229 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 175 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.8264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 60 HIS e 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.041768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041754 restraints weight = 360301.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041720 restraints weight = 702.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041717 restraints weight = 411.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041717 restraints weight = 362.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.041717 restraints weight = 362.733| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35909 Z= 0.104 Angle : 0.460 8.308 50016 Z= 0.259 Chirality : 0.043 0.142 6607 Planarity : 0.004 0.046 7196 Dihedral : 4.407 20.111 6913 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.45 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.10), residues: 6807 helix: 1.65 (0.12), residues: 1663 sheet: -1.52 (0.12), residues: 1875 loop : -1.78 (0.11), residues: 3269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 190 TYR 0.014 0.001 TYR b 490 PHE 0.011 0.001 PHE e 397 TRP 0.012 0.001 TRP a 79 HIS 0.003 0.001 HIS e 341 Details of bonding type rmsd covalent geometry : bond 0.00214 (35909) covalent geometry : angle 0.45956 (50016) hydrogen bonds : bond 0.03279 ( 2474) hydrogen bonds : angle 5.58691 ( 7068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.479 Fit side-chains revert: symmetry clash REVERT: L 59 LEU cc_start: 0.8866 (mm) cc_final: 0.8594 (tt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1638 time to fit residues: 43.5824 Evaluate side-chains 128 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 408 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 491 optimal weight: 10.0000 chunk 527 optimal weight: 30.0000 chunk 665 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 339 optimal weight: 0.9980 chunk 481 optimal weight: 0.0980 chunk 677 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.031646 restraints weight = 353144.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031594 restraints weight = 372028.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031594 restraints weight = 382148.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031594 restraints weight = 382149.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.031594 restraints weight = 382148.706| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35909 Z= 0.089 Angle : 0.427 6.337 50016 Z= 0.236 Chirality : 0.043 0.138 6607 Planarity : 0.003 0.042 7196 Dihedral : 3.710 17.474 6913 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.54 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.11), residues: 6807 helix: 2.52 (0.12), residues: 1678 sheet: -1.38 (0.12), residues: 1881 loop : -1.57 (0.11), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG h 57 TYR 0.014 0.001 TYR h 58 PHE 0.011 0.001 PHE b 397 TRP 0.005 0.000 TRP b 332 HIS 0.003 0.001 HIS L 60 Details of bonding type rmsd covalent geometry : bond 0.00198 (35909) covalent geometry : angle 0.42738 (50016) hydrogen bonds : bond 0.02805 ( 2474) hydrogen bonds : angle 4.74984 ( 7068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: h 58 TYR cc_start: 0.9153 (m-80) cc_final: 0.8945 (m-10) REVERT: e 389 LEU cc_start: 0.7181 (tt) cc_final: 0.6940 (tt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1654 time to fit residues: 43.7827 Evaluate side-chains 134 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 523 optimal weight: 50.0000 chunk 671 optimal weight: 0.6980 chunk 474 optimal weight: 30.0000 chunk 137 optimal weight: 40.0000 chunk 112 optimal weight: 40.0000 chunk 576 optimal weight: 7.9990 chunk 428 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 495 optimal weight: 50.0000 chunk 377 optimal weight: 20.0000 chunk 542 optimal weight: 20.0000 overall best weight: 15.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 237 GLN ** e 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039430 restraints weight = 372307.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039412 restraints weight = 422.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039411 restraints weight = 263.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039411 restraints weight = 196.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.039411 restraints weight = 196.593| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.8540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 35909 Z= 0.483 Angle : 0.843 14.023 50016 Z= 0.522 Chirality : 0.047 0.217 6607 Planarity : 0.007 0.106 7196 Dihedral : 6.905 33.339 6913 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.04 % Favored : 85.82 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.10), residues: 6807 helix: -0.71 (0.11), residues: 1629 sheet: -2.17 (0.12), residues: 1806 loop : -2.38 (0.11), residues: 3372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG b 492 TYR 0.080 0.003 TYR b 346 PHE 0.033 0.002 PHE f 975 TRP 0.033 0.003 TRP b 332 HIS 0.017 0.005 HIS e 35 Details of bonding type rmsd covalent geometry : bond 0.00770 (35909) covalent geometry : angle 0.84318 (50016) hydrogen bonds : bond 0.07575 ( 2474) hydrogen bonds : angle 8.18545 ( 7068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.415 Fit side-chains REVERT: h 58 TYR cc_start: 0.9270 (m-80) cc_final: 0.9014 (m-10) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1498 time to fit residues: 38.7925 Evaluate side-chains 130 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 556 optimal weight: 9.9990 chunk 471 optimal weight: 1.9990 chunk 518 optimal weight: 40.0000 chunk 7 optimal weight: 0.0770 chunk 123 optimal weight: 6.9990 chunk 595 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 416 optimal weight: 9.9990 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.040876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030580 restraints weight = 355012.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030580 restraints weight = 386115.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030580 restraints weight = 386113.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030580 restraints weight = 386113.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030580 restraints weight = 386113.623| |-----------------------------------------------------------------------------| r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.8158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35909 Z= 0.145 Angle : 0.510 11.614 50016 Z= 0.293 Chirality : 0.044 0.148 6607 Planarity : 0.004 0.100 7196 Dihedral : 5.108 27.413 6913 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.77 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.10), residues: 6807 helix: 0.98 (0.12), residues: 1663 sheet: -1.95 (0.12), residues: 1832 loop : -2.04 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 12 TYR 0.032 0.001 TYR h 58 PHE 0.018 0.001 PHE b 365 TRP 0.018 0.001 TRP a 79 HIS 0.008 0.001 HIS N 512 Details of bonding type rmsd covalent geometry : bond 0.00260 (35909) covalent geometry : angle 0.50952 (50016) hydrogen bonds : bond 0.03960 ( 2474) hydrogen bonds : angle 6.34609 ( 7068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.481 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1490 time to fit residues: 40.0417 Evaluate side-chains 127 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 33 optimal weight: 40.0000 chunk 108 optimal weight: 40.0000 chunk 495 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 479 optimal weight: 30.0000 chunk 433 optimal weight: 50.0000 chunk 444 optimal weight: 40.0000 chunk 218 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = 347220.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = 350236.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = 350629.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = 349209.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.040564 restraints weight = 349434.066| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5239 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35909 Z= 0.211 Angle : 0.543 13.073 50016 Z= 0.318 Chirality : 0.044 0.212 6607 Planarity : 0.004 0.093 7196 Dihedral : 5.170 27.481 6913 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.74 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.10), residues: 6807 helix: 1.02 (0.12), residues: 1656 sheet: -1.95 (0.12), residues: 1783 loop : -2.12 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 51 TYR 0.026 0.001 TYR b 455 PHE 0.015 0.001 PHE b 365 TRP 0.015 0.001 TRP b 332 HIS 0.008 0.002 HIS N 512 Details of bonding type rmsd covalent geometry : bond 0.00354 (35909) covalent geometry : angle 0.54327 (50016) hydrogen bonds : bond 0.04348 ( 2474) hydrogen bonds : angle 6.45046 ( 7068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13614 Ramachandran restraints generated. 6807 Oldfield, 0 Emsley, 6807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1447 time to fit residues: 37.9411 Evaluate side-chains 128 residues out of total 6170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 280 optimal weight: 0.0870 chunk 498 optimal weight: 40.0000 chunk 357 optimal weight: 40.0000 chunk 141 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 16 optimal weight: 0.0370 chunk 513 optimal weight: 30.0000 chunk 208 optimal weight: 30.0000 chunk 632 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 600 optimal weight: 30.0000 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = 343510.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = 344188.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = 341990.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = 338710.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.040993 restraints weight = 341911.327| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5175 moved from start: 0.8381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35909 Z= 0.140 Angle : 0.478 10.385 50016 Z= 0.272 Chirality : 0.043 0.144 6607 Planarity : 0.004 0.086 7196 Dihedral : 4.564 24.692 6913 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.55 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.10), residues: 6807 helix: 1.61 (0.12), residues: 1667 sheet: -1.87 (0.12), residues: 1772 loop : -1.98 (0.11), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG e 12 TYR 0.021 0.001 TYR b 455 PHE 0.022 0.001 PHE b 365 TRP 0.012 0.001 TRP a 79 HIS 0.006 0.001 HIS N 512 Details of bonding type rmsd covalent geometry : bond 0.00255 (35909) covalent geometry : angle 0.47766 (50016) hydrogen bonds : bond 0.03523 ( 2474) hydrogen bonds : angle 5.80927 ( 7068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.56 seconds wall clock time: 79 minutes 56.37 seconds (4796.37 seconds total)