Starting phenix.real_space_refine on Sat Feb 7 21:50:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.map" model { file = "/net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0y_63565/02_2026/9m0y_63565.cif" } resolution = 4.25 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= 0.024 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 4 5.16 5 C 21871 2.51 5 N 7121 2.21 5 O 7017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 36013 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2213 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 370} Link IDs: {'PTRANS': 8, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 1328 Unresolved non-hydrogen angles: 1696 Unresolved non-hydrogen dihedrals: 1123 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 18, 'TRP:plan': 7, 'GLN:plan1': 19, 'PHE:plan': 16, 'ASP:plan': 27, 'ASN:plan1': 22, 'GLU:plan': 24, 'TYR:plan': 20} Unresolved non-hydrogen planarities: 763 Chain: "B" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2182 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 375} Link IDs: {'PTRANS': 8, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 1362 Unresolved non-hydrogen angles: 1741 Unresolved non-hydrogen dihedrals: 1156 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'HIS:plan': 11, 'ARG:plan': 20, 'TRP:plan': 8, 'GLN:plan1': 19, 'PHE:plan': 16, 'ASP:plan': 27, 'ASN:plan1': 23, 'GLU:plan': 24, 'TYR:plan': 21} Unresolved non-hydrogen planarities: 792 Chain: "C" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 2715 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 461} Link IDs: {'PTRANS': 10, 'TRANS': 521} Chain breaks: 3 Unresolved non-hydrogen bonds: 1637 Unresolved non-hydrogen angles: 2081 Unresolved non-hydrogen dihedrals: 1369 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 35, 'ASN:plan1': 29, 'PHE:plan': 23, 'TYR:plan': 23, 'HIS:plan': 13, 'GLN:plan1': 22, 'ARG:plan': 23, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 948 Chain: "D" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 2519 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 444} Link IDs: {'PTRANS': 11, 'TRANS': 491} Chain breaks: 4 Unresolved non-hydrogen bonds: 1606 Unresolved non-hydrogen angles: 2044 Unresolved non-hydrogen dihedrals: 1358 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'ASN:plan1': 29, 'ASP:plan': 30, 'PHE:plan': 23, 'GLU:plan': 36, 'TYR:plan': 23, 'HIS:plan': 13, 'GLN:plan1': 20, 'ARG:plan': 22, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 938 Chain: "E" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 2704 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 10, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1609 Unresolved non-hydrogen angles: 2048 Unresolved non-hydrogen dihedrals: 1349 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'ASN:plan1': 30, 'ASP:plan': 34, 'PHE:plan': 23, 'GLU:plan': 35, 'TYR:plan': 22, 'HIS:plan': 12, 'GLN:plan1': 22, 'ARG:plan': 21, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 931 Chain: "F" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 2544 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 449} Link IDs: {'PTRANS': 11, 'TRANS': 496} Chain breaks: 4 Unresolved non-hydrogen bonds: 1626 Unresolved non-hydrogen angles: 2069 Unresolved non-hydrogen dihedrals: 1373 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLU:plan': 36, 'ASP:plan': 33, 'ASN:plan1': 29, 'PHE:plan': 23, 'TYR:plan': 23, 'HIS:plan': 13, 'GLN:plan1': 21, 'ARG:plan': 22, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 951 Chain: "G" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2173 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 379} Link IDs: {'PTRANS': 8, 'TRANS': 426} Chain breaks: 2 Unresolved non-hydrogen bonds: 1361 Unresolved non-hydrogen angles: 1735 Unresolved non-hydrogen dihedrals: 1151 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'ASP:plan': 25, 'ASN:plan1': 22, 'GLU:plan': 29, 'GLN:plan1': 16, 'HIS:plan': 10, 'PHE:plan': 16, 'ARG:plan': 20, 'TRP:plan': 7, 'TYR:plan': 21} Unresolved non-hydrogen planarities: 777 Chain: "J" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 2173 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 379} Link IDs: {'PTRANS': 8, 'TRANS': 426} Chain breaks: 2 Unresolved non-hydrogen bonds: 1362 Unresolved non-hydrogen angles: 1736 Unresolved non-hydrogen dihedrals: 1152 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'ASP:plan': 25, 'ASN:plan1': 22, 'GLU:plan': 29, 'GLN:plan1': 17, 'HIS:plan': 10, 'PHE:plan': 16, 'ARG:plan': 20, 'TRP:plan': 7, 'TYR:plan': 21} Unresolved non-hydrogen planarities: 781 Chain: "Q" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 786 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 133} Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 311 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': 4, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 202 Chain: "R" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 2976 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 384} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 498} Chain breaks: 1 Unresolved non-hydrogen bonds: 1358 Unresolved non-hydrogen angles: 1739 Unresolved non-hydrogen dihedrals: 1092 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ARG:plan': 35, 'ASN:plan1': 23, 'GLN:plan1': 22, 'HIS:plan': 11, 'GLU:plan': 28, 'PHE:plan': 23, 'ASP:plan': 27, 'TYR:plan': 11, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 813 Chain: "S" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 4313 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 647} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 795} Chain breaks: 1 Unresolved non-hydrogen bonds: 2220 Unresolved non-hydrogen angles: 2841 Unresolved non-hydrogen dihedrals: 1780 Unresolved non-hydrogen chiralities: 241 Planarities with less than four sites: {'TYR:plan': 23, 'ASN:plan1': 35, 'GLN:plan1': 32, 'HIS:plan': 15, 'PHE:plan': 27, 'GLU:plan': 69, 'ASP:plan': 40, 'ARG:plan': 31, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 1218 Chain: "T" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 811 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 133} Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASP:plan': 9, 'ASN:plan1': 7, 'TYR:plan': 4, 'PHE:plan': 3, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 179 Chain: "U" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3038 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 398} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 515} Chain breaks: 1 Unresolved non-hydrogen bonds: 1445 Unresolved non-hydrogen angles: 1851 Unresolved non-hydrogen dihedrals: 1175 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'ARG:plan': 38, 'GLN:plan1': 22, 'ASN:plan1': 23, 'HIS:plan': 14, 'GLU:plan': 28, 'PHE:plan': 29, 'ASP:plan': 29, 'TYR:plan': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 892 Chain: "V" Number of atoms: 4234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 823, 4234 Classifications: {'peptide': 823} Incomplete info: {'truncation_to_alanine': 665} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 795} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2308 Unresolved non-hydrogen angles: 2953 Unresolved non-hydrogen dihedrals: 1861 Unresolved non-hydrogen chiralities: 245 Planarities with less than four sites: {'TYR:plan': 23, 'ASN:plan1': 37, 'GLN:plan1': 31, 'HIS:plan': 17, 'PHE:plan': 33, 'GLU:plan': 69, 'ASP:plan': 40, 'ARG:plan': 33, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 1276 Chain: "j" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 299 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 84 Chain: "n" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 333 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 8.07, per 1000 atoms: 0.22 Number of scatterers: 36013 At special positions: 0 Unit cell: (359.55, 185.3, 108.8, 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 4 16.00 O 7017 8.00 N 7121 7.00 C 21871 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: 3.28 Conformation dependent library (CDL) restraints added in 2.1 seconds 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13136 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 115 sheets defined 25.3% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.779A pdb=" N PHE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 284 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 363 through 376 Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.594A pdb=" N THR A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'B' and resid 218 through 230 removed outlier: 3.745A pdb=" N PHE B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 284 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 363 through 376 Processing helix chain 'B' and resid 381 through 400 removed outlier: 3.557A pdb=" N THR B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 179 through 183 removed outlier: 4.044A pdb=" N HIS C 182 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 183 " --> pdb=" O ILE C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 179 through 183' Processing helix chain 'C' and resid 186 through 203 Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 234 through 302 removed outlier: 3.744A pdb=" N LEU C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 363 through 376 Processing helix chain 'C' and resid 383 through 400 removed outlier: 4.018A pdb=" N SER C 387 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 187 through 203 removed outlier: 3.993A pdb=" N GLN D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.788A pdb=" N GLU D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 302 removed outlier: 3.637A pdb=" N HIS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 363 Processing helix chain 'D' and resid 363 through 376 Processing helix chain 'D' and resid 383 through 400 removed outlier: 4.210A pdb=" N SER D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 456 Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 186 through 203 Processing helix chain 'E' and resid 217 through 229 removed outlier: 3.529A pdb=" N ASP E 229 " --> pdb=" O TRP E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 302 removed outlier: 3.711A pdb=" N LEU E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 363 removed outlier: 3.518A pdb=" N HIS E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 376 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.392A pdb=" N SER E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 456 Processing helix chain 'F' and resid 129 through 135 Processing helix chain 'F' and resid 156 through 167 Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 203 removed outlier: 3.915A pdb=" N ASN F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG F 199 " --> pdb=" O LYS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 302 removed outlier: 4.280A pdb=" N LEU F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 363 Processing helix chain 'F' and resid 363 through 376 removed outlier: 3.533A pdb=" N MET F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 400 removed outlier: 4.331A pdb=" N ALA F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 456 Processing helix chain 'G' and resid 234 through 302 removed outlier: 4.170A pdb=" N LEU G 302 " --> pdb=" O GLU G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 348 through 363 removed outlier: 3.570A pdb=" N HIS G 363 " --> pdb=" O ARG G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 363 through 376 Processing helix chain 'G' and resid 383 through 401 removed outlier: 3.758A pdb=" N SER G 387 " --> pdb=" O SER G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 456 Processing helix chain 'J' and resid 235 through 302 removed outlier: 4.093A pdb=" N LEU J 302 " --> pdb=" O GLU J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 363 Processing helix chain 'J' and resid 363 through 376 Processing helix chain 'J' and resid 383 through 401 Processing helix chain 'J' and resid 450 through 455 Processing helix chain 'Q' and resid 48 through 62 Processing helix chain 'Q' and resid 144 through 158 Processing helix chain 'Q' and resid 166 through 176 Processing helix chain 'Q' and resid 176 through 192 Processing helix chain 'R' and resid 19 through 27 removed outlier: 4.520A pdb=" N ARG R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG R 26 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 41 Processing helix chain 'R' and resid 42 through 45 Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.475A pdb=" N ALA R 93 " --> pdb=" O CYS R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 124 removed outlier: 5.046A pdb=" N PHE R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU R 122 " --> pdb=" O GLY R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 174 Processing helix chain 'R' and resid 216 through 220 Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.929A pdb=" N SER R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 311 Processing helix chain 'R' and resid 312 through 328 removed outlier: 4.580A pdb=" N ASP R 324 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLN R 325 " --> pdb=" O GLN R 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN R 328 " --> pdb=" O ASP R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 383 through 390 Processing helix chain 'R' and resid 393 through 399 removed outlier: 3.535A pdb=" N PHE R 397 " --> pdb=" O PHE R 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN R 399 " --> pdb=" O ASP R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 432 Processing helix chain 'R' and resid 435 through 446 removed outlier: 3.895A pdb=" N GLU R 439 " --> pdb=" O GLY R 435 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL R 441 " --> pdb=" O HIS R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 458 through 462 removed outlier: 3.688A pdb=" N ASP R 462 " --> pdb=" O PRO R 459 " (cutoff:3.500A) Processing helix chain 'S' and resid 251 through 256 removed outlier: 3.618A pdb=" N SER S 256 " --> pdb=" O ILE S 253 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 384 Processing helix chain 'S' and resid 985 through 990 Processing helix chain 'S' and resid 1044 through 1062 Processing helix chain 'S' and resid 1069 through 1074 Processing helix chain 'S' and resid 1091 through 1097 removed outlier: 3.521A pdb=" N PHE S1097 " --> pdb=" O LEU S1093 " (cutoff:3.500A) Processing helix chain 'S' and resid 1101 through 1110 Processing helix chain 'S' and resid 1125 through 1138 Processing helix chain 'T' and resid 48 through 62 Processing helix chain 'T' and resid 144 through 158 Processing helix chain 'T' and resid 166 through 176 Processing helix chain 'T' and resid 176 through 192 removed outlier: 3.583A pdb=" N GLN T 186 " --> pdb=" O ARG T 182 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP T 187 " --> pdb=" O MET T 183 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR T 188 " --> pdb=" O ALA T 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 28 removed outlier: 3.543A pdb=" N ARG U 21 " --> pdb=" O ASN U 17 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG U 24 " --> pdb=" O HIS U 20 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG U 25 " --> pdb=" O ARG U 21 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER U 28 " --> pdb=" O ARG U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 3.591A pdb=" N GLN U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE U 42 " --> pdb=" O GLN U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 45 No H-bonds generated for 'chain 'U' and resid 43 through 45' Processing helix chain 'U' and resid 89 through 93 removed outlier: 4.441A pdb=" N ALA U 93 " --> pdb=" O CYS U 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 124 removed outlier: 4.795A pdb=" N PHE U 121 " --> pdb=" O ARG U 117 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU U 122 " --> pdb=" O GLY U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 174 Processing helix chain 'U' and resid 263 through 272 removed outlier: 3.910A pdb=" N THR U 267 " --> pdb=" O ASP U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 272 through 282 Processing helix chain 'U' and resid 293 through 311 Processing helix chain 'U' and resid 312 through 328 removed outlier: 4.744A pdb=" N ASP U 324 " --> pdb=" O PHE U 320 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN U 325 " --> pdb=" O GLN U 321 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 353 Processing helix chain 'U' and resid 383 through 387 removed outlier: 3.551A pdb=" N LEU U 386 " --> pdb=" O SER U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 393 through 399 removed outlier: 3.640A pdb=" N PHE U 397 " --> pdb=" O PHE U 393 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN U 399 " --> pdb=" O ASP U 395 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 432 Processing helix chain 'U' and resid 436 through 446 removed outlier: 3.525A pdb=" N VAL U 441 " --> pdb=" O HIS U 437 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG U 442 " --> pdb=" O THR U 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 256 removed outlier: 3.626A pdb=" N SER V 256 " --> pdb=" O ILE V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 384 Processing helix chain 'V' and resid 985 through 991 Processing helix chain 'V' and resid 1044 through 1062 Processing helix chain 'V' and resid 1069 through 1074 Processing helix chain 'V' and resid 1091 through 1098 removed outlier: 3.856A pdb=" N LEU V1098 " --> pdb=" O ILE V1094 " (cutoff:3.500A) Processing helix chain 'V' and resid 1101 through 1110 Processing helix chain 'V' and resid 1125 through 1138 Processing helix chain 'j' and resid 53 through 65 removed outlier: 3.586A pdb=" N ARG j 57 " --> pdb=" O ASN j 53 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR j 58 " --> pdb=" O ILE j 54 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN j 62 " --> pdb=" O TYR j 58 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 66 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 412 removed outlier: 6.494A pdb=" N VAL A 727 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR A 410 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 725 " --> pdb=" O THR A 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 424 through 429 removed outlier: 3.511A pdb=" N ALA A 439 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 440 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 478 removed outlier: 6.221A pdb=" N SER A 489 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE A 476 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA A 487 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TRP A 478 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 485 " --> pdb=" O TRP A 478 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP A 499 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG A 505 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 521 removed outlier: 3.704A pdb=" N SER A 518 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER A 542 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 548 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 558 through 563 removed outlier: 4.128A pdb=" N CYS A 560 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS A 579 " --> pdb=" O CYS A 575 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 602 through 606 removed outlier: 4.410A pdb=" N TYR A 604 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 621 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN A 626 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N CYS A 632 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 648 through 651 removed outlier: 3.801A pdb=" N SER A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 405 through 412 removed outlier: 5.320A pdb=" N GLU B 729 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 424 through 429 removed outlier: 3.558A pdb=" N ALA B 439 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 437 " --> pdb=" O GLU B 428 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 440 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LYS B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 478 removed outlier: 5.331A pdb=" N ASP B 499 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B 505 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 516 through 521 removed outlier: 3.891A pdb=" N SER B 518 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER B 542 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER B 548 " --> pdb=" O SER B 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 560 through 563 removed outlier: 4.177A pdb=" N CYS B 560 " --> pdb=" O GLY B 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 605 through 606 removed outlier: 3.832A pdb=" N GLN B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN B 626 " --> pdb=" O CYS B 632 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS B 632 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 648 through 651 removed outlier: 3.866A pdb=" N SER B 663 " --> pdb=" O SER B 659 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'C' and resid 404 through 412 removed outlier: 6.371A pdb=" N VAL C 727 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR C 410 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 725 " --> pdb=" O THR C 410 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 424 through 428 removed outlier: 4.131A pdb=" N LYS C 444 " --> pdb=" O GLY C 440 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 478 removed outlier: 6.471A pdb=" N SER C 489 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE C 476 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA C 487 " --> pdb=" O ILE C 476 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 516 through 521 removed outlier: 3.827A pdb=" N SER C 518 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 530 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 537 " --> pdb=" O SER C 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 558 through 563 removed outlier: 3.588A pdb=" N ALA C 572 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 602 through 606 removed outlier: 3.830A pdb=" N TYR C 604 " --> pdb=" O ALA C 616 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 606 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 648 through 651 Processing sheet with id=AC7, first strand: chain 'D' and resid 146 through 148 removed outlier: 3.794A pdb=" N TYR D 147 " --> pdb=" O PHE D 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE D 155 " --> pdb=" O TYR D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 406 through 411 removed outlier: 6.204A pdb=" N GLU D 729 " --> pdb=" O PRO D 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 426 through 428 Processing sheet with id=AD1, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.799A pdb=" N VAL D 495 " --> pdb=" O VAL D 508 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL D 508 " --> pdb=" O VAL D 495 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU D 497 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 516 through 521 removed outlier: 4.535A pdb=" N SER D 518 " --> pdb=" O GLY D 532 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY D 532 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 541 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER D 542 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER D 548 " --> pdb=" O SER D 542 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 560 through 563 removed outlier: 3.605A pdb=" N HIS D 581 " --> pdb=" O PHE D 573 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 602 through 606 removed outlier: 3.874A pdb=" N TYR D 604 " --> pdb=" O ALA D 616 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN D 626 " --> pdb=" O CYS D 632 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N CYS D 632 " --> pdb=" O ASN D 626 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 648 through 651 Processing sheet with id=AD6, first strand: chain 'E' and resid 135 through 136 Processing sheet with id=AD7, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'E' and resid 404 through 412 removed outlier: 6.455A pdb=" N VAL E 727 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR E 410 " --> pdb=" O ILE E 725 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE E 725 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR E 724 " --> pdb=" O ASN E 720 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 718 " --> pdb=" O LYS E 726 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 702 " --> pdb=" O ALA E 719 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 424 through 429 removed outlier: 4.105A pdb=" N LYS E 444 " --> pdb=" O GLY E 440 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 473 through 478 removed outlier: 6.500A pdb=" N SER E 489 " --> pdb=" O SER E 474 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE E 476 " --> pdb=" O ALA E 487 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA E 487 " --> pdb=" O ILE E 476 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 495 " --> pdb=" O TYR E 509 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS E 507 " --> pdb=" O LEU E 497 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 516 through 521 removed outlier: 3.840A pdb=" N SER E 518 " --> pdb=" O GLY E 532 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER E 533 " --> pdb=" O LYS E 537 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS E 537 " --> pdb=" O SER E 533 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA E 550 " --> pdb=" O LEU E 540 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 558 through 562 removed outlier: 3.581A pdb=" N CYS E 560 " --> pdb=" O GLY E 574 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA E 572 " --> pdb=" O LYS E 562 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS E 579 " --> pdb=" O CYS E 575 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 602 through 606 removed outlier: 4.111A pdb=" N TYR E 604 " --> pdb=" O ALA E 616 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 616 " --> pdb=" O TYR E 604 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS E 606 " --> pdb=" O VAL E 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN E 621 " --> pdb=" O SER E 617 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN E 626 " --> pdb=" O CYS E 632 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N CYS E 632 " --> pdb=" O ASN E 626 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 648 through 651 Processing sheet with id=AE6, first strand: chain 'F' and resid 154 through 155 removed outlier: 3.652A pdb=" N PHE F 155 " --> pdb=" O TYR F 147 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 147 " --> pdb=" O PHE F 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 404 through 411 removed outlier: 4.456A pdb=" N VAL F 405 " --> pdb=" O VAL F 731 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL F 731 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU F 729 " --> pdb=" O PRO F 407 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 424 through 428 removed outlier: 3.669A pdb=" N GLY F 440 " --> pdb=" O LYS F 444 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS F 444 " --> pdb=" O GLY F 440 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 473 through 478 removed outlier: 3.816A pdb=" N CYS F 475 " --> pdb=" O SER F 489 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE F 496 " --> pdb=" O SER F 488 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 495 " --> pdb=" O VAL F 508 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL F 508 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU F 497 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 516 through 521 removed outlier: 4.052A pdb=" N SER F 518 " --> pdb=" O GLY F 532 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP F 541 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER F 542 " --> pdb=" O SER F 548 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N SER F 548 " --> pdb=" O SER F 542 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 558 through 563 removed outlier: 3.618A pdb=" N CYS F 560 " --> pdb=" O GLY F 574 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS F 581 " --> pdb=" O PHE F 573 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N CYS F 579 " --> pdb=" O CYS F 575 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 602 through 606 removed outlier: 4.082A pdb=" N TYR F 604 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 648 through 651 removed outlier: 3.515A pdb=" N ILE F 655 " --> pdb=" O TYR F 667 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 404 through 412 removed outlier: 5.210A pdb=" N VAL G 405 " --> pdb=" O VAL G 731 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL G 731 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU G 729 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA G 409 " --> pdb=" O VAL G 727 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 424 through 429 removed outlier: 4.187A pdb=" N GLY G 440 " --> pdb=" O LYS G 444 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS G 444 " --> pdb=" O GLY G 440 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 473 through 478 removed outlier: 3.646A pdb=" N TRP G 498 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 488 " --> pdb=" O ILE G 496 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR G 494 " --> pdb=" O ASP G 490 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP G 499 " --> pdb=" O ARG G 505 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG G 505 " --> pdb=" O ASP G 499 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 516 through 521 removed outlier: 4.161A pdb=" N SER G 518 " --> pdb=" O GLY G 532 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS G 537 " --> pdb=" O SER G 533 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER G 542 " --> pdb=" O SER G 548 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER G 548 " --> pdb=" O SER G 542 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 558 through 563 removed outlier: 3.684A pdb=" N CYS G 560 " --> pdb=" O GLY G 574 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL G 580 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL G 594 " --> pdb=" O VAL G 580 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR G 582 " --> pdb=" O ILE G 592 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 602 through 606 removed outlier: 3.789A pdb=" N TYR G 604 " --> pdb=" O ALA G 616 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 616 " --> pdb=" O TYR G 604 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU G 622 " --> pdb=" O SER G 635 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER G 635 " --> pdb=" O LEU G 622 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU G 624 " --> pdb=" O LEU G 633 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 648 through 651 Processing sheet with id=AG3, first strand: chain 'J' and resid 404 through 412 removed outlier: 5.080A pdb=" N VAL J 405 " --> pdb=" O VAL J 731 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL J 731 " --> pdb=" O VAL J 405 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU J 729 " --> pdb=" O PRO J 407 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA J 409 " --> pdb=" O VAL J 727 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 424 through 429 removed outlier: 4.039A pdb=" N GLY J 440 " --> pdb=" O LYS J 444 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS J 444 " --> pdb=" O GLY J 440 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 473 through 478 removed outlier: 3.561A pdb=" N SER J 488 " --> pdb=" O ILE J 496 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR J 494 " --> pdb=" O ASP J 490 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP J 499 " --> pdb=" O ARG J 505 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG J 505 " --> pdb=" O ASP J 499 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 516 through 521 removed outlier: 4.089A pdb=" N SER J 518 " --> pdb=" O GLY J 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU J 529 " --> pdb=" O TRP J 541 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS J 537 " --> pdb=" O SER J 533 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER J 542 " --> pdb=" O SER J 548 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N SER J 548 " --> pdb=" O SER J 542 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 562 through 563 removed outlier: 5.647A pdb=" N VAL J 580 " --> pdb=" O VAL J 594 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL J 594 " --> pdb=" O VAL J 580 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR J 582 " --> pdb=" O ILE J 592 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 602 through 606 removed outlier: 3.838A pdb=" N TYR J 604 " --> pdb=" O ALA J 616 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA J 616 " --> pdb=" O TYR J 604 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 648 through 651 Processing sheet with id=AH1, first strand: chain 'Q' and resid 67 through 71 Processing sheet with id=AH2, first strand: chain 'R' and resid 51 through 52 removed outlier: 6.941A pdb=" N THR R 51 " --> pdb=" O LEU R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'R' and resid 60 through 65 removed outlier: 6.701A pdb=" N ILE R 73 " --> pdb=" O ARG R 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU R 82 " --> pdb=" O ILE R 130 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE R 130 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE R 84 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 138 through 140 Processing sheet with id=AH5, first strand: chain 'R' and resid 138 through 140 removed outlier: 6.085A pdb=" N ASP R 197 " --> pdb=" O LEU R 203 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU R 203 " --> pdb=" O ASP R 197 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 222 through 225 removed outlier: 3.622A pdb=" N LEU R 229 " --> pdb=" O PHE R 242 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE R 239 " --> pdb=" O THR R 255 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR R 255 " --> pdb=" O ILE R 239 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL R 241 " --> pdb=" O VAL R 253 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'R' and resid 330 through 335 removed outlier: 6.005A pdb=" N MET R 331 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR R 347 " --> pdb=" O MET R 331 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA R 377 " --> pdb=" O VAL R 367 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 487 through 488 removed outlier: 3.519A pdb=" N ILE R 501 " --> pdb=" O ILE R 487 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 517 through 522 Processing sheet with id=AI1, first strand: chain 'S' and resid 1007 through 1008 removed outlier: 3.837A pdb=" N THR S1041 " --> pdb=" O TYR S 5 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN S 4 " --> pdb=" O ILE S1089 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 17 through 21 removed outlier: 6.594A pdb=" N LEU S 39 " --> pdb=" O GLU S 54 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU S 54 " --> pdb=" O LEU S 39 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE S 41 " --> pdb=" O VAL S 52 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 61 through 67 removed outlier: 3.649A pdb=" N VAL S 63 " --> pdb=" O LEU S 80 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN S 85 " --> pdb=" O THR S 81 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S' and resid 61 through 67 removed outlier: 3.649A pdb=" N VAL S 63 " --> pdb=" O LEU S 80 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN S 85 " --> pdb=" O THR S 81 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY S 106 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'S' and resid 130 through 132 Processing sheet with id=AI6, first strand: chain 'S' and resid 164 through 169 removed outlier: 6.842A pdb=" N VAL S 181 " --> pdb=" O ILE S 165 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL S 167 " --> pdb=" O CYS S 179 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS S 179 " --> pdb=" O VAL S 167 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE S 169 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR S 177 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR S 193 " --> pdb=" O ILE S 178 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR S 182 " --> pdb=" O HIS S 189 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS S 189 " --> pdb=" O TYR S 182 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 210 " --> pdb=" O VAL S 190 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 218 through 220 Processing sheet with id=AI8, first strand: chain 'S' and resid 258 through 263 removed outlier: 3.513A pdb=" N CYS S 260 " --> pdb=" O GLY S 274 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG S 279 " --> pdb=" O ASP S 275 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU S 280 " --> pdb=" O LEU S 304 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU S 304 " --> pdb=" O LEU S 280 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET S 282 " --> pdb=" O VAL S 302 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL S 302 " --> pdb=" O MET S 282 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU S 284 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU S 300 " --> pdb=" O LEU S 284 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLU S 286 " --> pdb=" O LYS S 298 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'S' and resid 311 through 318 removed outlier: 3.690A pdb=" N THR S 315 " --> pdb=" O PHE S 323 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL S 321 " --> pdb=" O LEU S 317 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER S 331 " --> pdb=" O THR S 352 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR S 352 " --> pdb=" O SER S 331 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU S 333 " --> pdb=" O MET S 350 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'S' and resid 359 through 365 removed outlier: 4.025A pdb=" N ASP S 361 " --> pdb=" O CYS S 378 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'S' and resid 720 through 721 removed outlier: 3.639A pdb=" N SER S 720 " --> pdb=" O SER S 738 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 725 through 727 removed outlier: 3.584A pdb=" N LEU S 792 " --> pdb=" O VAL S 735 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N HIS S 789 " --> pdb=" O GLN S 806 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLN S 806 " --> pdb=" O HIS S 789 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU S 791 " --> pdb=" O ALA S 804 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA S 804 " --> pdb=" O LEU S 791 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE S 793 " --> pdb=" O LEU S 802 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER S 762 " --> pdb=" O ALA S 804 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N GLN S 806 " --> pdb=" O SER S 762 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N SER S 764 " --> pdb=" O GLN S 806 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'S' and resid 811 through 818 removed outlier: 6.194A pdb=" N GLY S 832 " --> pdb=" O LEU S 814 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU S 816 " --> pdb=" O ILE S 830 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE S 830 " --> pdb=" O LEU S 816 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER S 818 " --> pdb=" O TYR S 828 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR S 828 " --> pdb=" O SER S 818 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN S 852 " --> pdb=" O THR S 860 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR S 860 " --> pdb=" O GLN S 852 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER S 854 " --> pdb=" O LEU S 858 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU S 858 " --> pdb=" O SER S 854 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 870 through 876 removed outlier: 4.990A pdb=" N SER S 872 " --> pdb=" O SER S 883 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL S 888 " --> pdb=" O ASN S 904 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN S 904 " --> pdb=" O VAL S 888 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU S 890 " --> pdb=" O GLU S 902 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'S' and resid 913 through 917 removed outlier: 4.017A pdb=" N TYR S 913 " --> pdb=" O GLY S 924 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL S 930 " --> pdb=" O ARG S 947 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ARG S 947 " --> pdb=" O VAL S 930 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU S 932 " --> pdb=" O ILE S 945 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU S 992 " --> pdb=" O ILE S 945 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG S 947 " --> pdb=" O LEU S 992 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 954 through 958 removed outlier: 4.278A pdb=" N ALA S 956 " --> pdb=" O ALA S 968 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA S 968 " --> pdb=" O ALA S 956 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU S 958 " --> pdb=" O LEU S 966 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU S 969 " --> pdb=" O ASN S 973 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN S 973 " --> pdb=" O GLU S 969 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 1076 through 1077 Processing sheet with id=AJ9, first strand: chain 'S' and resid 1113 through 1114 Processing sheet with id=AK1, first strand: chain 'T' and resid 67 through 71 removed outlier: 3.652A pdb=" N ASP T 99 " --> pdb=" O THR T 114 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'U' and resid 104 through 105 removed outlier: 6.782A pdb=" N THR U 51 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS U 544 " --> pdb=" O ALA U 529 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'U' and resid 60 through 65 removed outlier: 6.758A pdb=" N ILE U 73 " --> pdb=" O ARG U 63 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU U 82 " --> pdb=" O ILE U 130 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE U 130 " --> pdb=" O LEU U 82 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE U 84 " --> pdb=" O LEU U 128 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'U' and resid 138 through 140 Processing sheet with id=AK5, first strand: chain 'U' and resid 138 through 140 removed outlier: 6.138A pdb=" N ASP U 197 " --> pdb=" O LEU U 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU U 203 " --> pdb=" O ASP U 197 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'U' and resid 222 through 225 removed outlier: 3.628A pdb=" N LEU U 229 " --> pdb=" O PHE U 242 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE U 239 " --> pdb=" O THR U 255 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR U 255 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL U 241 " --> pdb=" O VAL U 253 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'U' and resid 329 through 331 removed outlier: 3.848A pdb=" N ALA U 377 " --> pdb=" O VAL U 367 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN U 369 " --> pdb=" O VAL U 375 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL U 375 " --> pdb=" O ASN U 369 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'U' and resid 466 through 467 removed outlier: 3.999A pdb=" N TYR U 490 " --> pdb=" O SER U 467 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA U 491 " --> pdb=" O LEU U 497 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU U 497 " --> pdb=" O ALA U 491 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'V' and resid 1004 through 1008 removed outlier: 3.957A pdb=" N VAL V1006 " --> pdb=" O GLY V1031 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR V1041 " --> pdb=" O TYR V 5 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN V 4 " --> pdb=" O ILE V1089 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'V' and resid 17 through 21 removed outlier: 6.504A pdb=" N LEU V 39 " --> pdb=" O GLU V 54 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU V 54 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE V 41 " --> pdb=" O VAL V 52 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'V' and resid 63 through 67 removed outlier: 3.706A pdb=" N VAL V 63 " --> pdb=" O LEU V 80 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA V 86 " --> pdb=" O HIS V 105 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N HIS V 105 " --> pdb=" O ALA V 86 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE V 88 " --> pdb=" O ARG V 103 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'V' and resid 123 through 124 removed outlier: 3.525A pdb=" N VAL V 142 " --> pdb=" O PHE V 155 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'V' and resid 164 through 169 removed outlier: 6.662A pdb=" N VAL V 181 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL V 167 " --> pdb=" O CYS V 179 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS V 179 " --> pdb=" O VAL V 167 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE V 180 " --> pdb=" O LYS V 191 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS V 191 " --> pdb=" O PHE V 180 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'V' and resid 216 through 220 Processing sheet with id=AL6, first strand: chain 'V' and resid 258 through 262 removed outlier: 3.601A pdb=" N CYS V 260 " --> pdb=" O GLY V 274 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU V 280 " --> pdb=" O LEU V 305 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU V 288 " --> pdb=" O LEU V 297 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU V 297 " --> pdb=" O GLU V 288 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'V' and resid 311 through 313 removed outlier: 3.738A pdb=" N CYS V 313 " --> pdb=" O GLY V 325 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY V 325 " --> pdb=" O CYS V 313 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER V 331 " --> pdb=" O THR V 352 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR V 352 " --> pdb=" O SER V 331 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU V 333 " --> pdb=" O MET V 350 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'V' and resid 359 through 365 removed outlier: 3.923A pdb=" N ASP V 361 " --> pdb=" O CYS V 378 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'V' and resid 720 through 721 removed outlier: 3.722A pdb=" N SER V 720 " --> pdb=" O SER V 738 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'V' and resid 725 through 727 removed outlier: 7.859A pdb=" N HIS V 789 " --> pdb=" O GLN V 806 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN V 806 " --> pdb=" O HIS V 789 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU V 791 " --> pdb=" O ALA V 804 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA V 804 " --> pdb=" O LEU V 791 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE V 793 " --> pdb=" O LEU V 802 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER V 762 " --> pdb=" O ALA V 804 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN V 806 " --> pdb=" O SER V 762 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER V 764 " --> pdb=" O GLN V 806 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'V' and resid 811 through 819 removed outlier: 6.433A pdb=" N GLY V 832 " --> pdb=" O LEU V 814 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU V 816 " --> pdb=" O ILE V 830 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE V 830 " --> pdb=" O LEU V 816 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER V 818 " --> pdb=" O TYR V 828 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR V 828 " --> pdb=" O SER V 818 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN V 852 " --> pdb=" O THR V 860 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR V 860 " --> pdb=" O GLN V 852 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N SER V 854 " --> pdb=" O LEU V 858 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU V 858 " --> pdb=" O SER V 854 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'V' and resid 870 through 876 removed outlier: 4.577A pdb=" N SER V 872 " --> pdb=" O SER V 883 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL V 888 " --> pdb=" O ASN V 904 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN V 904 " --> pdb=" O VAL V 888 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU V 890 " --> pdb=" O GLU V 902 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'V' and resid 914 through 917 removed outlier: 6.920A pdb=" N LEU V 932 " --> pdb=" O ILE V 945 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'V' and resid 954 through 959 removed outlier: 6.996A pdb=" N ALA V 968 " --> pdb=" O SER V 955 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL V 957 " --> pdb=" O LEU V 966 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU V 966 " --> pdb=" O VAL V 957 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN V 978 " --> pdb=" O GLU V 994 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU V 994 " --> pdb=" O GLN V 978 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'V' and resid 1076 through 1077 Processing sheet with id=AM7, first strand: chain 'V' and resid 1113 through 1114 2357 hydrogen bonds defined for protein. 6600 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: 11.24 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6970 1.31 - 1.44: 7872 1.44 - 1.56: 21476 1.56 - 1.68: 0 1.68 - 1.81: 6 Bond restraints: 36324 Sorted by residual: bond pdb=" CA ARG V 114 " pdb=" CB ARG V 114 " ideal model delta sigma weight residual 1.532 1.451 0.081 1.67e-02 3.59e+03 2.35e+01 bond pdb=" CA ILE V 112 " pdb=" C ILE V 112 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.27e-02 6.20e+03 2.07e+01 bond pdb=" C ARG V 114 " pdb=" O ARG V 114 " ideal model delta sigma weight residual 1.245 1.187 0.058 1.53e-02 4.27e+03 1.42e+01 bond pdb=" C ILE V 112 " pdb=" O ILE V 112 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" CB ARG V 114 " pdb=" CG ARG V 114 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.30e+00 ... (remaining 36319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 49841 1.92 - 3.84: 717 3.84 - 5.76: 35 5.76 - 7.68: 8 7.68 - 9.60: 4 Bond angle restraints: 50605 Sorted by residual: angle pdb=" C ARG V 114 " pdb=" N PRO V 115 " pdb=" CA PRO V 115 " ideal model delta sigma weight residual 119.85 125.83 -5.98 1.01e+00 9.80e-01 3.51e+01 angle pdb=" N GLY V 113 " pdb=" CA GLY V 113 " pdb=" C GLY V 113 " ideal model delta sigma weight residual 110.42 118.45 -8.03 1.49e+00 4.50e-01 2.91e+01 angle pdb=" C GLU S 151 " pdb=" CA GLU S 151 " pdb=" CB GLU S 151 " ideal model delta sigma weight residual 116.63 110.62 6.01 1.16e+00 7.43e-01 2.69e+01 angle pdb=" C LEU D 235 " pdb=" CA LEU D 235 " pdb=" CB LEU D 235 " ideal model delta sigma weight residual 117.23 110.71 6.52 1.36e+00 5.41e-01 2.30e+01 angle pdb=" N LEU U 387 " pdb=" CA LEU U 387 " pdb=" C LEU U 387 " ideal model delta sigma weight residual 114.04 108.16 5.88 1.24e+00 6.50e-01 2.25e+01 ... (remaining 50600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 20818 16.77 - 33.54: 276 33.54 - 50.31: 234 50.31 - 67.08: 6 67.08 - 83.85: 1 Dihedral angle restraints: 21335 sinusoidal: 1298 harmonic: 20037 Sorted by residual: dihedral pdb=" N ARG V 114 " pdb=" C ARG V 114 " pdb=" CA ARG V 114 " pdb=" CB ARG V 114 " ideal model delta harmonic sigma weight residual 122.80 107.53 15.27 0 2.50e+00 1.60e-01 3.73e+01 dihedral pdb=" CA VAL U 371 " pdb=" C VAL U 371 " pdb=" N THR U 372 " pdb=" CA THR U 372 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CG ARG V 114 " pdb=" CD ARG V 114 " pdb=" NE ARG V 114 " pdb=" CZ ARG V 114 " ideal model delta sinusoidal sigma weight residual 90.00 39.56 50.44 2 1.50e+01 4.44e-03 1.27e+01 ... (remaining 21332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4813 0.040 - 0.080: 1166 0.080 - 0.120: 629 0.120 - 0.161: 10 0.161 - 0.201: 2 Chirality restraints: 6620 Sorted by residual: chirality pdb=" CA ILE V 112 " pdb=" N ILE V 112 " pdb=" C ILE V 112 " pdb=" CB ILE V 112 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ARG V 114 " pdb=" N ARG V 114 " pdb=" C ARG V 114 " pdb=" CB ARG V 114 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA VAL D 246 " pdb=" N VAL D 246 " pdb=" C VAL D 246 " pdb=" CB VAL D 246 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 6617 not shown) Planarity restraints: 7274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 247 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C GLN D 247 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN D 247 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS D 248 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J 525 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO J 526 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO J 526 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 526 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 525 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO G 526 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 526 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 526 " 0.027 5.00e-02 4.00e+02 ... (remaining 7271 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 848 2.70 - 3.25: 32850 3.25 - 3.80: 54156 3.80 - 4.35: 52155 4.35 - 4.90: 97096 Nonbonded interactions: 237105 Sorted by model distance: nonbonded pdb=" NH1 ARG R 488 " pdb=" O PHE R 489 " model vdw 2.155 3.120 nonbonded pdb=" O ASP S 110 " pdb=" OH TYR S 136 " model vdw 2.204 3.040 nonbonded pdb=" O GLY V 119 " pdb=" NH2 ARG V 134 " model vdw 2.208 3.120 nonbonded pdb=" O SER G 659 " pdb=" N VAL G 700 " model vdw 2.236 3.120 nonbonded pdb=" O SER J 659 " pdb=" N VAL J 700 " model vdw 2.253 3.120 ... (remaining 237100 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 'A' and (resid 234 through 400 or (resid 401 through 406 and (name N or n \ ame CA or name C or name O or name CB )) or resid 407 through 411 or (resid 424 \ through 439 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 0 through 477 or (resid 478 through 492 and (name N or name CA or name C or name \ O or name CB )) or resid 493 through 704 or (resid 705 through 708 and (name N \ or name CA or name C or name O or name CB )) or resid 709 through 713 or (resid \ 714 through 722 and (name N or name CA or name C or name O or name CB )) or resi \ d 723 through 731)) selection = (chain 'B' and (resid 234 through 411 or (resid 424 through 439 and (name N or n \ ame CA or name C or name O or name CB )) or resid 440 through 477 or (resid 478 \ through 492 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 3 through 731)) selection = (chain 'D' and (resid 181 or resid 235 through 284 or resid 347 through 411 or r \ esid 424 through 679 or resid 700 through 731)) selection = (chain 'F' and (resid 234 through 284 or resid 347 through 411 or resid 424 thro \ ugh 679 or resid 700 through 731)) selection = (chain 'G' and (resid 234 through 284 or resid 347 through 411 or resid 424 thro \ ugh 731)) selection = (chain 'J' and (resid 234 through 284 or resid 347 through 411 or resid 424 thro \ ugh 731)) } ncs_group { reference = (chain 'C' and (resid 131 through 525 or (resid 526 through 531 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 532 through 564 and (name N o \ r name CA or name C or name O or name CB )) or resid 565 through 650 or (resid 6 \ 51 and (name N or name CA or name C or name O or name CB )) or resid 652 through \ 682 or resid 697 through 731)) selection = (chain 'E' and (resid 131 through 488 or (resid 489 through 491 and (name N or n \ ame CA or name C or name O or name CB )) or resid 492 through 504 or (resid 505 \ through 506 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 7 through 539 or (resid 540 through 564 and (name N or name CA or name C or name \ O or name CB )) or resid 565 through 568 or (resid 569 through 573 and (name N \ or name CA or name C or name O or name CB )) or (resid 574 through 590 and (name \ N or name CA or name C or name O or name CB )) or resid 591 through 731)) } ncs_group { reference = chain 'Q' selection = (chain 'T' and (resid 47 through 90 or (resid 91 through 92 and (name N or name \ CA or name C or name O or name CB )) or (resid 93 through 103 and (name N or nam \ e CA or name C or name O or name CB )) or resid 104 through 184 or (resid 185 th \ rough 186 and (name N or name CA or name C or name O or name CB )) or resid 187 \ through 189 or (resid 190 and (name N or name CA or name C or name O or name CB \ )) or resid 191 through 193)) } ncs_group { reference = (chain 'R' and (resid 11 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 or (resid 47 and ( \ name N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 thr \ ough 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thr \ ough 123 or (resid 124 through 136 and (name N or name CA or name C or name O or \ name CB )) or resid 137 through 219 or resid 221 through 345 or (resid 346 thro \ ugh 358 and (name N or name CA or name C or name O or name CB )) or resid 359 th \ rough 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 484 or (resid 485 and (name N or name CA or name C or name \ O or name CB )) or resid 486 through 487 or (resid 488 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 name C or name O or name CB )) or resi \ d 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 'U' and (resid 11 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 273 or resid 290 through 338 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 3 \ 93 or (resid 394 through 396 and (name N or name CA or name C or name O or name \ CB )) or resid 397 through 401 or (resid 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 through \ 418 and (name N or name CA or name C or name O or name CB )) or resid 419 throu \ gh 450 or (resid 451 through 452 and (name N or name CA or name C or name O or n \ ame CB )) or resid 453 through 497 or (resid 498 through 503 and (name N or name \ CA or name C or name O or name CB )) or resid 504 through 548)) } ncs_group { reference = (chain 'S' and (resid 1 through 50 or (resid 51 through 55 and (name N or name C \ A or name C or name O or name CB )) or resid 56 through 132 or (resid 133 and (n \ ame N or name CA or name C or name O or name CB )) or resid 134 through 142 or ( \ resid 143 and (name N or name CA or name C or name O or name CB )) or resid 144 \ through 154 or (resid 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 through 178 or (resid 179 and (name N or name CA or name C or na \ me O or name CB )) or resid 180 through 187 or (resid 188 through 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 788 or (resi \ d 789 through 821 and (name N or name CA or name C or name O or name CB )) or re \ sid 822 through 909 or (resid 910 through 917 and (name N or name CA or name C o \ r name O or name CB )) or (resid 918 through 936 and (name N or name CA or name \ C or name O or name CB )) or resid 937 through 953 or (resid 954 through 966 and \ (name N or name CA or name C or name O or name CB )) or (resid 967 through 995 \ and (name N or name CA or name C or name O or name CB )) or resid 996 or (resid \ 997 through 1000 and (name N or name CA or name C or name O or name CB )) or (re \ sid 1001 through 1009 and (name N or name CA or name C or name O or name CB )) o \ r resid 1010 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 'V' and (resid 1 through 59 or (resid 60 through 68 and (name N or name C \ A or name C or name O or name CB )) or resid 69 through 82 or (resid 83 and (nam \ e N or name CA or name C or name O or name CB )) or resid 84 through 119 or (res \ id 120 through 121 and (name N or name CA or name C or name O or name CB )) or r \ esid 122 through 163 or (resid 164 through 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 through 182 or (resid 183 through 184 and ( \ name N or name CA or name C or name O or name CB )) or resid 185 through 188 or \ (resid 189 through 204 and (name N or name CA or name C or name O or name CB )) \ or resid 205 through 1140)) } ncs_group { reference = (chain 'j' and resid 4 through 65) selection = (chain 'n' and ((resid 4 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 19 or (resid 34 through 36 and (name \ N or name CA or name C or name O or name CB )) or resid 37 through 51 or (resid \ 52 and (name N or name CA or name C or name O or name CB )) or resid 53 through \ 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or res \ id 59 through 65)) } 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: 43.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 36.560 Find NCS groups from input model: 1.030 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 36324 Z= 0.121 Angle : 0.516 9.595 50605 Z= 0.300 Chirality : 0.042 0.201 6620 Planarity : 0.004 0.050 7274 Dihedral : 8.773 83.850 8199 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.51 % Favored : 97.41 % Rotamer: Outliers : 0.21 % Allowed : 0.41 % Favored : 99.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.93 % 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: 0.98 (0.11), residues: 6821 helix: 3.62 (0.12), residues: 1666 sheet: 0.10 (0.12), residues: 2008 loop : -0.62 (0.11), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 114 TYR 0.013 0.001 TYR E 569 PHE 0.010 0.001 PHE R 520 TRP 0.016 0.001 TRP R 36 HIS 0.006 0.001 HIS R 523 Details of bonding type rmsd covalent geometry : bond 0.00256 (36324) covalent geometry : angle 0.51565 (50605) hydrogen bonds : bond 0.21573 ( 2343) hydrogen bonds : angle 7.71198 ( 6600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.405 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 142 average time/residue: 0.1469 time to fit residues: 40.1425 Evaluate side-chains 134 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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: 3.9990 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 40.0000 chunk 310 optimal weight: 50.0000 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 30.0000 chunk 597 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 49 ASN ** R 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 HIS U 415 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028820 restraints weight = 515369.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028813 restraints weight = 554712.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028813 restraints weight = 557156.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028813 restraints weight = 557157.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028813 restraints weight = 557157.079| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36324 Z= 0.278 Angle : 0.639 10.738 50605 Z= 0.369 Chirality : 0.045 0.163 6620 Planarity : 0.006 0.067 7274 Dihedral : 4.484 33.341 6932 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 0.21 % Allowed : 7.39 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: 0.06 (0.11), residues: 6821 helix: 2.83 (0.12), residues: 1645 sheet: -0.63 (0.12), residues: 2026 loop : -1.00 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG V 114 TYR 0.026 0.002 TYR S 182 PHE 0.023 0.002 PHE R 425 TRP 0.016 0.002 TRP C 498 HIS 0.011 0.003 HIS V 189 Details of bonding type rmsd covalent geometry : bond 0.00488 (36324) covalent geometry : angle 0.63887 (50605) hydrogen bonds : bond 0.04554 ( 2343) hydrogen bonds : angle 5.89184 ( 6600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.467 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1503 time to fit residues: 38.7651 Evaluate side-chains 128 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 13 optimal weight: 8.9990 chunk 571 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 604 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 chunk 338 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 315 optimal weight: 40.0000 chunk 399 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 523 HIS U 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028880 restraints weight = 523799.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028878 restraints weight = 564359.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028878 restraints weight = 564609.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028878 restraints weight = 564609.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028878 restraints weight = 564609.367| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36324 Z= 0.160 Angle : 0.501 9.844 50605 Z= 0.274 Chirality : 0.043 0.161 6620 Planarity : 0.004 0.060 7274 Dihedral : 3.802 34.922 6932 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: 0.17 (0.11), residues: 6821 helix: 3.21 (0.12), residues: 1644 sheet: -0.72 (0.12), residues: 2014 loop : -0.98 (0.11), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 190 TYR 0.024 0.001 TYR T 91 PHE 0.016 0.001 PHE S 972 TRP 0.012 0.001 TRP E 498 HIS 0.011 0.001 HIS R 523 Details of bonding type rmsd covalent geometry : bond 0.00307 (36324) covalent geometry : angle 0.50134 (50605) hydrogen bonds : bond 0.03765 ( 2343) hydrogen bonds : angle 5.17620 ( 6600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.435 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1533 time to fit residues: 39.5785 Evaluate side-chains 125 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 412 optimal weight: 5.9990 chunk 410 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 438 optimal weight: 30.0000 chunk 617 optimal weight: 40.0000 chunk 544 optimal weight: 4.9990 chunk 606 optimal weight: 6.9990 chunk 640 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 624 optimal weight: 40.0000 chunk 251 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 37 HIS R 44 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027713 restraints weight = 555244.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027611 restraints weight = 600816.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027611 restraints weight = 638988.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027611 restraints weight = 638988.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027611 restraints weight = 638988.414| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 36324 Z= 0.293 Angle : 0.659 13.974 50605 Z= 0.381 Chirality : 0.045 0.177 6620 Planarity : 0.006 0.113 7274 Dihedral : 5.300 40.136 6932 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.74 % Favored : 91.19 % Rotamer: Outliers : 0.21 % Allowed : 9.86 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -0.92 (0.10), residues: 6821 helix: 2.01 (0.12), residues: 1621 sheet: -1.22 (0.12), residues: 1937 loop : -1.58 (0.11), residues: 3263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.002 ARG n 57 TYR 0.036 0.002 TYR R 455 PHE 0.031 0.002 PHE U 365 TRP 0.028 0.002 TRP C 517 HIS 0.015 0.002 HIS R 523 Details of bonding type rmsd covalent geometry : bond 0.00515 (36324) covalent geometry : angle 0.65882 (50605) hydrogen bonds : bond 0.05006 ( 2343) hydrogen bonds : angle 6.39944 ( 6600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.258 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1407 time to fit residues: 35.0805 Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 411 optimal weight: 20.0000 chunk 508 optimal weight: 6.9990 chunk 626 optimal weight: 50.0000 chunk 155 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 163 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 430 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 267 optimal weight: 50.0000 chunk 51 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 399 ASN V 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.034215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.028436 restraints weight = 543024.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028209 restraints weight = 617140.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028081 restraints weight = 694099.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.028047 restraints weight = 758443.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.028013 restraints weight = 773684.331| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36324 Z= 0.219 Angle : 0.568 11.404 50605 Z= 0.319 Chirality : 0.044 0.170 6620 Planarity : 0.005 0.062 7274 Dihedral : 4.677 37.524 6932 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -0.88 (0.10), residues: 6821 helix: 2.19 (0.13), residues: 1632 sheet: -1.32 (0.12), residues: 1917 loop : -1.57 (0.11), residues: 3272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG E 586 TYR 0.030 0.001 TYR n 58 PHE 0.019 0.001 PHE U 365 TRP 0.027 0.002 TRP n 63 HIS 0.010 0.002 HIS E 570 Details of bonding type rmsd covalent geometry : bond 0.00393 (36324) covalent geometry : angle 0.56763 (50605) hydrogen bonds : bond 0.04086 ( 2343) hydrogen bonds : angle 5.93538 ( 6600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.426 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1407 time to fit residues: 35.2053 Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 127 optimal weight: 4.9990 chunk 420 optimal weight: 7.9990 chunk 527 optimal weight: 20.0000 chunk 664 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 504 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 30 optimal weight: 50.0000 chunk 550 optimal weight: 9.9990 chunk 188 optimal weight: 50.0000 chunk 412 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 453 GLN V 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.033147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.027516 restraints weight = 551997.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.027424 restraints weight = 630096.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.027413 restraints weight = 666266.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.027403 restraints weight = 670566.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.027403 restraints weight = 674858.379| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 36324 Z= 0.296 Angle : 0.656 11.998 50605 Z= 0.380 Chirality : 0.045 0.206 6620 Planarity : 0.005 0.069 7274 Dihedral : 5.570 40.290 6932 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.75 % Favored : 89.18 % Rotamer: Outliers : 0.21 % Allowed : 4.52 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -1.56 (0.10), residues: 6821 helix: 1.42 (0.13), residues: 1610 sheet: -1.54 (0.12), residues: 1780 loop : -2.00 (0.10), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG n 57 TYR 0.032 0.002 TYR E 509 PHE 0.039 0.002 PHE R 365 TRP 0.031 0.002 TRP C 498 HIS 0.022 0.003 HIS V 189 Details of bonding type rmsd covalent geometry : bond 0.00515 (36324) covalent geometry : angle 0.65561 (50605) hydrogen bonds : bond 0.05054 ( 2343) hydrogen bonds : angle 6.82132 ( 6600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.370 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.1489 time to fit residues: 36.6481 Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 131 optimal weight: 30.0000 chunk 559 optimal weight: 0.8980 chunk 541 optimal weight: 0.0470 chunk 358 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 334 optimal weight: 30.0000 chunk 497 optimal weight: 30.0000 chunk 632 optimal weight: 7.9990 chunk 333 optimal weight: 30.0000 chunk 670 optimal weight: 30.0000 chunk 263 optimal weight: 5.9990 overall best weight: 4.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** 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 = 0.2950 r_free = 0.2950 target = 0.033626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027931 restraints weight = 542125.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.027849 restraints weight = 655597.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027819 restraints weight = 684495.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027789 restraints weight = 700868.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027789 restraints weight = 716745.380| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 36324 Z= 0.190 Angle : 0.544 9.910 50605 Z= 0.306 Chirality : 0.044 0.179 6620 Planarity : 0.004 0.061 7274 Dihedral : 4.769 38.520 6932 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -1.25 (0.10), residues: 6821 helix: 1.94 (0.13), residues: 1626 sheet: -1.57 (0.12), residues: 1834 loop : -1.82 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 586 TYR 0.025 0.001 TYR E 569 PHE 0.020 0.001 PHE U 365 TRP 0.016 0.001 TRP C 498 HIS 0.007 0.002 HIS V 163 Details of bonding type rmsd covalent geometry : bond 0.00344 (36324) covalent geometry : angle 0.54441 (50605) hydrogen bonds : bond 0.03937 ( 2343) hydrogen bonds : angle 6.07721 ( 6600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.511 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1549 time to fit residues: 37.7037 Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 260 optimal weight: 20.0000 chunk 522 optimal weight: 30.0000 chunk 530 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 534 optimal weight: 30.0000 chunk 181 optimal weight: 30.0000 chunk 285 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 645 optimal weight: 20.0000 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 341 HIS ** U 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.032071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.026810 restraints weight = 563316.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.026520 restraints weight = 633196.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.026519 restraints weight = 738189.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.026519 restraints weight = 738532.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.026519 restraints weight = 738532.024| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.186 36324 Z= 0.470 Angle : 0.849 13.675 50605 Z= 0.507 Chirality : 0.048 0.323 6620 Planarity : 0.007 0.106 7274 Dihedral : 6.925 41.971 6932 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.53 % Favored : 85.40 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.05 % 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: -2.77 (0.10), residues: 6821 helix: -0.15 (0.12), residues: 1574 sheet: -2.08 (0.12), residues: 1663 loop : -2.55 (0.10), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG V 114 TYR 0.065 0.003 TYR R 468 PHE 0.057 0.003 PHE R 365 TRP 0.072 0.003 TRP C 498 HIS 0.017 0.004 HIS V 189 Details of bonding type rmsd covalent geometry : bond 0.00817 (36324) covalent geometry : angle 0.84883 (50605) hydrogen bonds : bond 0.06922 ( 2343) hydrogen bonds : angle 8.31172 ( 6600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1370 time to fit residues: 33.5392 Evaluate side-chains 121 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 651 optimal weight: 40.0000 chunk 549 optimal weight: 10.0000 chunk 669 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 392 optimal weight: 9.9990 chunk 536 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 408 optimal weight: 0.0370 chunk 474 optimal weight: 20.0000 overall best weight: 4.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** 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 = 0.2932 r_free = 0.2932 target = 0.032965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027401 restraints weight = 556345.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027245 restraints weight = 659089.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027245 restraints weight = 724855.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027245 restraints weight = 724855.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.027245 restraints weight = 724855.574| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 36324 Z= 0.195 Angle : 0.565 10.049 50605 Z= 0.320 Chirality : 0.044 0.185 6620 Planarity : 0.005 0.065 7274 Dihedral : 5.202 36.724 6932 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -1.90 (0.10), residues: 6821 helix: 1.23 (0.13), residues: 1621 sheet: -1.98 (0.12), residues: 1734 loop : -2.13 (0.11), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 488 TYR 0.023 0.001 TYR E 569 PHE 0.027 0.001 PHE R 365 TRP 0.033 0.002 TRP C 498 HIS 0.007 0.002 HIS R 523 Details of bonding type rmsd covalent geometry : bond 0.00354 (36324) covalent geometry : angle 0.56467 (50605) hydrogen bonds : bond 0.04168 ( 2343) hydrogen bonds : angle 6.63444 ( 6600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.129 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1346 time to fit residues: 33.1394 Evaluate side-chains 122 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 168 optimal weight: 20.0000 chunk 609 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 585 optimal weight: 0.0050 chunk 34 optimal weight: 10.0000 chunk 637 optimal weight: 50.0000 chunk 547 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 573 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** 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 = 0.2937 r_free = 0.2937 target = 0.033079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026851 restraints weight = 539565.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026851 restraints weight = 585426.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026851 restraints weight = 585519.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026851 restraints weight = 585519.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.026851 restraints weight = 585519.349| |-----------------------------------------------------------------------------| r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 36324 Z= 0.175 Angle : 0.531 8.756 50605 Z= 0.298 Chirality : 0.044 0.178 6620 Planarity : 0.005 0.064 7274 Dihedral : 4.713 35.507 6932 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.78 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -1.59 (0.10), residues: 6821 helix: 1.77 (0.13), residues: 1633 sheet: -1.88 (0.12), residues: 1732 loop : -2.06 (0.11), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 488 TYR 0.022 0.001 TYR R 468 PHE 0.018 0.001 PHE R 365 TRP 0.031 0.002 TRP C 498 HIS 0.006 0.001 HIS R 544 Details of bonding type rmsd covalent geometry : bond 0.00322 (36324) covalent geometry : angle 0.53143 (50605) hydrogen bonds : bond 0.03823 ( 2343) hydrogen bonds : angle 6.13684 ( 6600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13642 Ramachandran restraints generated. 6821 Oldfield, 0 Emsley, 6821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.468 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1481 time to fit residues: 36.5394 Evaluate side-chains 122 residues out of total 6168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 259 optimal weight: 20.0000 chunk 467 optimal weight: 40.0000 chunk 188 optimal weight: 20.0000 chunk 573 optimal weight: 0.0020 chunk 408 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 545 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 556 optimal weight: 0.0000 chunk 657 optimal weight: 9.9990 chunk 393 optimal weight: 3.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.033220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.027065 restraints weight = 528795.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.026994 restraints weight = 571225.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.026994 restraints weight = 592127.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.026994 restraints weight = 592199.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.026994 restraints weight = 592199.761| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36324 Z= 0.168 Angle : 0.516 7.942 50605 Z= 0.287 Chirality : 0.044 0.157 6620 Planarity : 0.004 0.067 7274 Dihedral : 4.422 33.560 6932 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.93 % 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: -1.34 (0.11), residues: 6821 helix: 2.25 (0.13), residues: 1621 sheet: -1.92 (0.12), residues: 1779 loop : -1.91 (0.11), residues: 3421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 488 TYR 0.022 0.001 TYR R 468 PHE 0.019 0.001 PHE R 365 TRP 0.033 0.002 TRP C 498 HIS 0.005 0.001 HIS R 523 Details of bonding type rmsd covalent geometry : bond 0.00311 (36324) covalent geometry : angle 0.51563 (50605) hydrogen bonds : bond 0.03630 ( 2343) hydrogen bonds : angle 5.76135 ( 6600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6571.17 seconds wall clock time: 112 minutes 52.52 seconds (6772.52 seconds total)