Starting phenix.real_space_refine on Fri Mar 6 05:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o85_0651/03_2026/6o85_0651.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 Cl 4 4.86 5 C 18349 2.51 5 N 4832 2.21 5 O 5267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28576 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3172 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 407} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 27, 'GLU:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 3994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 3994 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 730 Unresolved non-hydrogen angles: 946 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ARG:plan': 34, 'GLU:plan': 24, 'ASN:plan1': 10, 'GLN:plan1': 16, 'ASP:plan': 11, 'PHE:plan': 9, 'TYR:plan': 5, 'HIS:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 461 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2415 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 20, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2425 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 20, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2712 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2713 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2025 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 12, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "H" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2025 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 12, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "I" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1609 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 2, 'GLU:plan': 7, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "L" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 25, 'ASP:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "S" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2096 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1075 Unresolved non-hydrogen angles: 1375 Unresolved non-hydrogen dihedrals: 846 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'ASP:plan': 15, 'HIS:plan': 9, 'GLU:plan': 26, 'ARG:plan': 19, 'GLN:plan1': 13, 'ASN:plan1': 14, 'PHE:plan': 6, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 443 Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 6.29, per 1000 atoms: 0.22 Number of scatterers: 28576 At special positions: 0 Unit cell: (123.3, 149.604, 228.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 124 16.00 O 5267 8.00 N 4832 7.00 C 18349 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7786 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 43 sheets defined 43.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.626A pdb=" N LEU A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.520A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.972A pdb=" N CYS A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.696A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.984A pdb=" N SER A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.613A pdb=" N GLN B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 Processing helix chain 'B' and resid 268 through 278 removed outlier: 3.852A pdb=" N VAL B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 550 through 568 Processing helix chain 'B' and resid 570 through 586 Processing helix chain 'B' and resid 588 through 606 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 613 through 628 removed outlier: 4.052A pdb=" N TYR B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 657 through 661 removed outlier: 5.153A pdb=" N ILE B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 671 removed outlier: 3.514A pdb=" N LEU B 667 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 687 Processing helix chain 'B' and resid 693 through 699 Processing helix chain 'B' and resid 700 through 715 removed outlier: 3.540A pdb=" N GLU B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.737A pdb=" N MET C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.918A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.576A pdb=" N GLY C 98 " --> pdb=" O GLY C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.692A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.962A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 208 removed outlier: 3.600A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.695A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 304' Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.835A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.861A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.583A pdb=" N GLY D 98 " --> pdb=" O GLY D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 145 removed outlier: 3.517A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 158 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 208 removed outlier: 4.080A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.601A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 304' Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'E' and resid 191 through 196 removed outlier: 4.089A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.529A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 325 removed outlier: 3.663A pdb=" N ALA E 296 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN E 325 " --> pdb=" O ARG E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 353 removed outlier: 3.552A pdb=" N GLY E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.982A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.601A pdb=" N ASP E 462 " --> pdb=" O ASP E 459 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 459 through 463' Processing helix chain 'E' and resid 475 through 479 removed outlier: 3.680A pdb=" N ASN E 478 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 518 removed outlier: 3.559A pdb=" N LEU E 516 " --> pdb=" O VAL E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.767A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.331A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 292 through 325 removed outlier: 5.398A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN F 325 " --> pdb=" O ARG F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 353 removed outlier: 3.745A pdb=" N SER F 343 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 378 removed outlier: 3.760A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.893A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 520 removed outlier: 3.550A pdb=" N LEU F 516 " --> pdb=" O VAL F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 21 through 38 removed outlier: 3.602A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'G' and resid 62 through 83 removed outlier: 3.986A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.613A pdb=" N CYS G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.521A pdb=" N LYS G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.718A pdb=" N LEU G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.636A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 21 through 38 removed outlier: 3.603A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS H 38 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'H' and resid 62 through 83 removed outlier: 3.986A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 105 removed outlier: 3.613A pdb=" N CYS H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.521A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.719A pdb=" N LEU H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 247 through 251 Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.636A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 46 removed outlier: 3.540A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.903A pdb=" N GLU I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 3.519A pdb=" N ILE I 93 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 97 removed outlier: 3.645A pdb=" N LEU I 97 " --> pdb=" O TYR I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 94 through 97' Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.799A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.686A pdb=" N LEU I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.671A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'I' and resid 229 through 236 Processing helix chain 'I' and resid 282 through 292 removed outlier: 4.288A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.540A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 removed outlier: 3.903A pdb=" N GLU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 3.517A pdb=" N ILE J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 removed outlier: 3.646A pdb=" N LEU J 97 " --> pdb=" O TYR J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.799A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.687A pdb=" N LEU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.672A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'J' and resid 229 through 236 Processing helix chain 'J' and resid 282 through 292 removed outlier: 4.288A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP J 292 " --> pdb=" O ASP J 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 61 removed outlier: 3.593A pdb=" N LYS L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU L 61 " --> pdb=" O ILE L 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 57 through 61' Processing helix chain 'L' and resid 90 through 119 Processing helix chain 'L' and resid 122 through 134 Processing helix chain 'L' and resid 134 through 142 Processing helix chain 'L' and resid 145 through 158 removed outlier: 3.790A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 165 removed outlier: 3.545A pdb=" N SER L 164 " --> pdb=" O ILE L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 183 removed outlier: 3.756A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 242 through 264 removed outlier: 3.832A pdb=" N SER L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS L 264 " --> pdb=" O LYS L 260 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 62 Processing helix chain 'S' and resid 137 through 146 removed outlier: 3.729A pdb=" N LEU S 141 " --> pdb=" O GLY S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 179 removed outlier: 3.728A pdb=" N GLN S 169 " --> pdb=" O CYS S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 214 removed outlier: 3.602A pdb=" N GLN S 212 " --> pdb=" O LEU S 208 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 243 Processing helix chain 'd' and resid 4 through 16 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 124 removed outlier: 7.556A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN A 44 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL A 151 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 46 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 removed outlier: 5.750A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 217 removed outlier: 3.576A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ALA A 204 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 215 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 202 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 4.023A pdb=" N PHE A 224 " --> pdb=" O ILE I 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE I 182 " --> pdb=" O PHE A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.795A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.199A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.728A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.154A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.151A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.522A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.522A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN B 44 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL B 151 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL B 46 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AB5, first strand: chain 'B' and resid 212 through 217 removed outlier: 3.967A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.810A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.491A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 418 through 419 removed outlier: 7.626A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 329 through 331 removed outlier: 5.953A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL C 189 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N MET C 217 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 191 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AC3, first strand: chain 'D' and resid 329 through 331 removed outlier: 5.881A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AC5, first strand: chain 'E' and resid 383 through 387 removed outlier: 6.419A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.586A pdb=" N SER E 416 " --> pdb=" O ASP E 490 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP E 490 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 383 through 387 removed outlier: 6.485A pdb=" N ASP F 331 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL F 359 " --> pdb=" O ASP F 331 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 407 through 408 removed outlier: 3.659A pdb=" N VAL F 414 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 175 through 178 removed outlier: 8.467A pdb=" N THR G 176 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY G 196 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 200 removed outlier: 3.613A pdb=" N ILE G 206 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP G 274 " --> pdb=" O ASN G 208 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 175 through 178 removed outlier: 8.468A pdb=" N THR H 176 " --> pdb=" O PHE H 148 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY H 196 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 199 through 200 removed outlier: 3.613A pdb=" N ILE H 206 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP H 274 " --> pdb=" O ASN H 208 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 75 through 78 removed outlier: 3.521A pdb=" N ILE I 78 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 200 through 201 removed outlier: 3.609A pdb=" N VAL I 200 " --> pdb=" O ARG I 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG I 133 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LYS I 268 " --> pdb=" O MET I 130 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET I 132 " --> pdb=" O LYS I 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 75 through 78 removed outlier: 3.520A pdb=" N ILE J 78 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 200 through 201 removed outlier: 3.609A pdb=" N VAL J 200 " --> pdb=" O ARG J 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG J 133 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LYS J 268 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET J 132 " --> pdb=" O LYS J 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'L' and resid 18 through 26 removed outlier: 6.979A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE L 26 " --> pdb=" O GLY L 30 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU L 42 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU L 84 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR L 81 " --> pdb=" O VAL L 75 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL L 75 " --> pdb=" O TYR L 81 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP L 83 " --> pdb=" O ILE L 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 190 through 191 Processing sheet with id=AE1, first strand: chain 'L' and resid 224 through 227 Processing sheet with id=AE2, first strand: chain 'S' and resid 42 through 46 removed outlier: 3.501A pdb=" N GLY S 82 " --> pdb=" O ASP S 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 89 through 90 Processing sheet with id=AE4, first strand: chain 'S' and resid 155 through 159 removed outlier: 7.172A pdb=" N ALA S 155 " --> pdb=" O LEU S 186 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU S 188 " --> pdb=" O ALA S 155 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU S 157 " --> pdb=" O LEU S 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AE6, first strand: chain 'S' and resid 300 through 302 Processing sheet with id=AE7, first strand: chain 'S' and resid 376 through 377 removed outlier: 3.528A pdb=" N PHE S 376 " --> pdb=" O TRP S 456 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU S 443 " --> pdb=" O ILE S 454 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TRP S 456 " --> pdb=" O ILE S 441 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE S 441 " --> pdb=" O TRP S 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA S 442 " --> pdb=" O ASN S 407 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN S 407 " --> pdb=" O ALA S 442 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG S 446 " --> pdb=" O VAL S 403 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N VAL S 403 " --> pdb=" O ARG S 446 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N THR S 413 " --> pdb=" O PRO S 432 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY S 415 " --> pdb=" O THR S 430 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR S 430 " --> pdb=" O GLY S 415 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL S 417 " --> pdb=" O VAL S 428 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL S 428 " --> pdb=" O VAL S 417 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA S 419 " --> pdb=" O LYS S 426 " (cutoff:3.500A) removed outlier: 11.064A pdb=" N LEU S 429 " --> pdb=" O GLU S 372 " (cutoff:3.500A) removed outlier: 10.863A pdb=" N GLU S 372 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ASN S 431 " --> pdb=" O GLU S 370 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU S 370 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL S 433 " --> pdb=" O PHE S 368 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N PHE S 368 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE S 465 " --> pdb=" O PHE S 368 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU S 370 " --> pdb=" O VAL S 463 " (cutoff:3.500A) 1304 hydrogen bonds defined for protein. 3744 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: 5.49 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4891 1.31 - 1.43: 6853 1.43 - 1.56: 17089 1.56 - 1.68: 6 1.68 - 1.81: 193 Bond restraints: 29032 Sorted by residual: bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" CD2 TRP B 628 " pdb=" CE2 TRP B 628 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.94e+01 ... (remaining 29027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 39061 3.48 - 6.97: 341 6.97 - 10.45: 36 10.45 - 13.93: 23 13.93 - 17.42: 4 Bond angle restraints: 39465 Sorted by residual: angle pdb=" CD2 TRP A 317 " pdb=" CE3 TRP A 317 " pdb=" CZ3 TRP A 317 " ideal model delta sigma weight residual 118.60 129.45 -10.85 1.30e+00 5.92e-01 6.97e+01 angle pdb=" CD2 TRP A 397 " pdb=" CE3 TRP A 397 " pdb=" CZ3 TRP A 397 " ideal model delta sigma weight residual 118.60 129.44 -10.84 1.30e+00 5.92e-01 6.95e+01 angle pdb=" CD2 TRP F 476 " pdb=" CE3 TRP F 476 " pdb=" CZ3 TRP F 476 " ideal model delta sigma weight residual 118.60 129.43 -10.83 1.30e+00 5.92e-01 6.94e+01 angle pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " pdb=" CZ3 TRP L 135 " ideal model delta sigma weight residual 118.60 129.42 -10.82 1.30e+00 5.92e-01 6.92e+01 angle pdb=" CD2 TRP F 350 " pdb=" CE3 TRP F 350 " pdb=" CZ3 TRP F 350 " ideal model delta sigma weight residual 118.60 129.42 -10.82 1.30e+00 5.92e-01 6.92e+01 ... (remaining 39460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 17048 29.64 - 59.28: 310 59.28 - 88.91: 30 88.91 - 118.55: 12 118.55 - 148.19: 2 Dihedral angle restraints: 17402 sinusoidal: 5530 harmonic: 11872 Sorted by residual: dihedral pdb=" CA ILE F 198 " pdb=" C ILE F 198 " pdb=" N PRO F 199 " pdb=" CA PRO F 199 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE E 198 " pdb=" C ILE E 198 " pdb=" N PRO E 199 " pdb=" CA PRO E 199 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN D 242 " pdb=" C ASN D 242 " pdb=" N GLY D 243 " pdb=" CA GLY D 243 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 17399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 4864 1.017 - 2.034: 0 2.034 - 3.050: 0 3.050 - 4.067: 0 4.067 - 5.084: 4 Chirality restraints: 4868 Sorted by residual: chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.61 5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.61 5.08 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.43 4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 4865 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO F 396 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO E 396 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 292 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO H 293 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 293 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 293 " -0.037 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4892 2.77 - 3.30: 25527 3.30 - 3.84: 47457 3.84 - 4.37: 52148 4.37 - 4.90: 92388 Nonbonded interactions: 222412 Sorted by model distance: nonbonded pdb=" OG SER D 30 " pdb=" OE1 GLU D 33 " model vdw 2.239 3.040 nonbonded pdb=" O LEU H 73 " pdb=" OG SER H 77 " model vdw 2.253 3.040 nonbonded pdb=" O LEU G 73 " pdb=" OG SER G 77 " model vdw 2.253 3.040 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.273 3.040 nonbonded pdb=" O SER D 17 " pdb=" OG1 THR D 21 " model vdw 2.312 3.040 ... (remaining 222407 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 'C' and resid 8 through 351) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 10.080 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.920 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 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 : 0.005 0.122 29032 Z= 0.258 Angle : 0.871 17.417 39465 Z= 0.509 Chirality : 0.153 5.084 4868 Planarity : 0.006 0.074 5057 Dihedral : 12.825 148.190 9616 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.89 % Allowed : 4.73 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -3.78 (0.11), residues: 4046 helix: -2.57 (0.09), residues: 1587 sheet: -2.25 (0.20), residues: 575 loop : -2.44 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 56 TYR 0.028 0.001 TYR G 275 PHE 0.033 0.002 PHE C 177 TRP 0.025 0.002 TRP G 272 HIS 0.009 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00498 (29032) covalent geometry : angle 0.87052 (39465) hydrogen bonds : bond 0.13948 ( 1296) hydrogen bonds : angle 6.65559 ( 3744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 PRO cc_start: 0.7643 (Cg_exo) cc_final: 0.7087 (Cg_endo) REVERT: A 276 LEU cc_start: 0.8192 (tp) cc_final: 0.7981 (tp) REVERT: C 45 ILE cc_start: 0.7724 (mt) cc_final: 0.7123 (mt) REVERT: D 11 LEU cc_start: 0.7140 (tp) cc_final: 0.6759 (tp) REVERT: H 32 GLU cc_start: 0.6288 (tp30) cc_final: 0.6079 (tm-30) REVERT: H 93 MET cc_start: 0.6227 (mtt) cc_final: 0.5622 (tmm) REVERT: J 105 SER cc_start: 0.4945 (p) cc_final: 0.4669 (t) REVERT: J 263 ILE cc_start: 0.7096 (mt) cc_final: 0.6895 (mm) REVERT: L 7 PHE cc_start: 0.7664 (m-10) cc_final: 0.7238 (m-10) REVERT: L 82 ILE cc_start: 0.8156 (mt) cc_final: 0.7905 (mt) outliers start: 23 outliers final: 3 residues processed: 878 average time/residue: 0.1540 time to fit residues: 226.3042 Evaluate side-chains 524 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 521 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 0.0070 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS B 63 GLN B 72 ASN C 154 GLN C 252 HIS C 261 HIS D 138 ASN D 345 HIS E 265 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN F 430 HIS F 479 HIS H 13 GLN H 223 ASN J 190 HIS L 40 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119027 restraints weight = 53684.267| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.59 r_work: 0.3650 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29032 Z= 0.150 Angle : 0.602 10.355 39465 Z= 0.327 Chirality : 0.045 0.159 4868 Planarity : 0.004 0.061 5057 Dihedral : 6.021 176.381 4134 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.45 % Allowed : 13.87 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4046 helix: -0.40 (0.12), residues: 1617 sheet: -2.00 (0.20), residues: 582 loop : -1.79 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 53 TYR 0.028 0.001 TYR H 252 PHE 0.024 0.002 PHE C 177 TRP 0.014 0.002 TRP G 272 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00319 (29032) covalent geometry : angle 0.60222 (39465) hydrogen bonds : bond 0.02954 ( 1296) hydrogen bonds : angle 4.24497 ( 3744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 553 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8547 (tp) cc_final: 0.8244 (tp) REVERT: A 394 THR cc_start: 0.8200 (m) cc_final: 0.7955 (p) REVERT: C 45 ILE cc_start: 0.8058 (mt) cc_final: 0.7675 (mt) REVERT: E 175 SER cc_start: 0.7329 (t) cc_final: 0.7114 (t) REVERT: E 238 GLN cc_start: 0.8097 (tp40) cc_final: 0.7763 (tt0) REVERT: F 200 SER cc_start: 0.7415 (m) cc_final: 0.6559 (p) REVERT: F 251 ASP cc_start: 0.8513 (t0) cc_final: 0.7957 (t70) REVERT: H 32 GLU cc_start: 0.6354 (tp30) cc_final: 0.5967 (tm-30) REVERT: H 93 MET cc_start: 0.6508 (mtt) cc_final: 0.5521 (tmm) REVERT: H 109 ASN cc_start: 0.7298 (m-40) cc_final: 0.6895 (p0) REVERT: H 213 ASN cc_start: 0.8717 (t0) cc_final: 0.8454 (t0) REVERT: I 2 GLU cc_start: 0.6787 (tt0) cc_final: 0.6580 (tp30) REVERT: I 49 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: J 132 MET cc_start: 0.8660 (mpp) cc_final: 0.8397 (mmm) REVERT: J 263 ILE cc_start: 0.7489 (mt) cc_final: 0.7277 (mm) REVERT: L 76 ASP cc_start: 0.7633 (t0) cc_final: 0.7263 (t0) REVERT: L 82 ILE cc_start: 0.8280 (mt) cc_final: 0.8046 (mt) outliers start: 89 outliers final: 52 residues processed: 615 average time/residue: 0.1470 time to fit residues: 152.8398 Evaluate side-chains 520 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 467 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 437 CYS Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 262 ASP Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain S residue 315 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 5.9990 chunk 378 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 287 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 337 HIS B 63 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN D 188 HIS D 309 HIS E 234 GLN E 422 GLN E 430 HIS E 431 ASN F 254 ASN F 477 GLN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS L 40 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.138245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109487 restraints weight = 87966.398| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.95 r_work: 0.3460 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29032 Z= 0.173 Angle : 0.636 14.182 39465 Z= 0.343 Chirality : 0.047 0.451 4868 Planarity : 0.004 0.057 5057 Dihedral : 5.795 176.256 4130 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 4.15 % Allowed : 15.07 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.13), residues: 4046 helix: 0.61 (0.13), residues: 1625 sheet: -1.67 (0.21), residues: 603 loop : -1.45 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 56 TYR 0.016 0.001 TYR A 128 PHE 0.027 0.002 PHE H 100 TRP 0.011 0.001 TRP J 37 HIS 0.007 0.001 HIS I 203 Details of bonding type rmsd covalent geometry : bond 0.00371 (29032) covalent geometry : angle 0.63591 (39465) hydrogen bonds : bond 0.02981 ( 1296) hydrogen bonds : angle 3.85647 ( 3744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 509 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.8542 (tt) cc_final: 0.8323 (mt) REVERT: B 307 SER cc_start: 0.9089 (m) cc_final: 0.8736 (p) REVERT: B 352 HIS cc_start: 0.7133 (m-70) cc_final: 0.6696 (t70) REVERT: C 45 ILE cc_start: 0.8409 (mt) cc_final: 0.8045 (mt) REVERT: C 226 MET cc_start: 0.8909 (tpt) cc_final: 0.8489 (tpt) REVERT: D 58 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6592 (mpp) REVERT: E 175 SER cc_start: 0.8144 (t) cc_final: 0.7898 (t) REVERT: E 238 GLN cc_start: 0.8501 (tp40) cc_final: 0.8235 (tt0) REVERT: F 200 SER cc_start: 0.7914 (m) cc_final: 0.7105 (p) REVERT: F 251 ASP cc_start: 0.8671 (t0) cc_final: 0.8063 (t70) REVERT: F 461 ASP cc_start: 0.8751 (m-30) cc_final: 0.8514 (m-30) REVERT: H 20 MET cc_start: 0.6672 (tpp) cc_final: 0.6387 (ttm) REVERT: H 32 GLU cc_start: 0.6379 (tp30) cc_final: 0.5919 (tm-30) REVERT: H 70 GLU cc_start: 0.8110 (tp30) cc_final: 0.7879 (tm-30) REVERT: H 202 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8515 (tm-30) REVERT: H 245 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6297 (t0) REVERT: I 2 GLU cc_start: 0.7053 (tt0) cc_final: 0.6414 (tp30) REVERT: I 49 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: J 50 GLU cc_start: 0.8778 (pt0) cc_final: 0.8560 (tm-30) REVERT: L 20 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7418 (tmm) REVERT: L 111 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7595 (tt) outliers start: 107 outliers final: 65 residues processed: 585 average time/residue: 0.1574 time to fit residues: 155.2012 Evaluate side-chains 490 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 501 ILE Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 241 LEU Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 386 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 310 optimal weight: 0.4980 chunk 326 optimal weight: 0.0170 chunk 95 optimal weight: 30.0000 chunk 170 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN L 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.137131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108594 restraints weight = 66955.124| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.29 r_work: 0.3474 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29032 Z= 0.138 Angle : 0.545 14.340 39465 Z= 0.301 Chirality : 0.044 0.156 4868 Planarity : 0.003 0.048 5057 Dihedral : 5.575 172.790 4130 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.72 % Allowed : 16.82 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.42 (0.13), residues: 4046 helix: 1.25 (0.13), residues: 1631 sheet: -1.44 (0.21), residues: 610 loop : -1.27 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 52 TYR 0.010 0.001 TYR J 264 PHE 0.025 0.001 PHE I 121 TRP 0.009 0.001 TRP J 37 HIS 0.006 0.001 HIS G 170 Details of bonding type rmsd covalent geometry : bond 0.00286 (29032) covalent geometry : angle 0.54461 (39465) hydrogen bonds : bond 0.02428 ( 1296) hydrogen bonds : angle 3.63493 ( 3744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 434 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 159 ILE cc_start: 0.8666 (tt) cc_final: 0.8452 (mt) REVERT: B 352 HIS cc_start: 0.7210 (m-70) cc_final: 0.6841 (t70) REVERT: B 433 SER cc_start: 0.8049 (m) cc_final: 0.7601 (p) REVERT: C 45 ILE cc_start: 0.8465 (mt) cc_final: 0.8030 (mt) REVERT: C 226 MET cc_start: 0.8878 (tpt) cc_final: 0.8537 (tpt) REVERT: C 320 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8138 (mp) REVERT: D 19 VAL cc_start: 0.8286 (p) cc_final: 0.7943 (m) REVERT: D 212 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7888 (mm) REVERT: D 292 GLU cc_start: 0.8334 (tp30) cc_final: 0.7955 (tp30) REVERT: D 314 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8173 (t0) REVERT: E 238 GLN cc_start: 0.8494 (tp40) cc_final: 0.8272 (tt0) REVERT: F 200 SER cc_start: 0.7944 (m) cc_final: 0.7143 (p) REVERT: G 154 GLU cc_start: 0.8336 (pt0) cc_final: 0.8098 (pt0) REVERT: H 20 MET cc_start: 0.6918 (tpp) cc_final: 0.6626 (ttm) REVERT: H 32 GLU cc_start: 0.6434 (tp30) cc_final: 0.5992 (tm-30) REVERT: H 70 GLU cc_start: 0.8163 (tp30) cc_final: 0.7833 (tm-30) REVERT: H 164 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7844 (tpp) REVERT: H 202 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8461 (tm-30) REVERT: H 245 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6713 (t0) REVERT: H 250 PHE cc_start: 0.4647 (m-10) cc_final: 0.4260 (m-10) REVERT: I 49 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: J 125 ASP cc_start: 0.8311 (t0) cc_final: 0.7809 (t0) REVERT: J 189 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8256 (mtmm) outliers start: 96 outliers final: 63 residues processed: 497 average time/residue: 0.1551 time to fit residues: 129.5189 Evaluate side-chains 465 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 396 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 193 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 44 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 150 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 chunk 401 optimal weight: 0.0980 chunk 324 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 201 HIS C 309 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.126778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096826 restraints weight = 82126.701| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.59 r_work: 0.3258 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29032 Z= 0.214 Angle : 0.664 14.141 39465 Z= 0.358 Chirality : 0.048 0.293 4868 Planarity : 0.004 0.052 5057 Dihedral : 6.014 174.126 4130 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.65 % Allowed : 16.78 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.31 (0.13), residues: 4046 helix: 1.31 (0.13), residues: 1632 sheet: -1.33 (0.21), residues: 595 loop : -1.19 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 53 TYR 0.025 0.002 TYR A 128 PHE 0.022 0.002 PHE H 75 TRP 0.018 0.002 TRP J 37 HIS 0.010 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00485 (29032) covalent geometry : angle 0.66353 (39465) hydrogen bonds : bond 0.03257 ( 1296) hydrogen bonds : angle 3.87122 ( 3744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 413 time to evaluate : 0.940 Fit side-chains REVERT: A 295 GLU cc_start: 0.8747 (pm20) cc_final: 0.8498 (mp0) REVERT: A 384 HIS cc_start: 0.7806 (m-70) cc_final: 0.7447 (t70) REVERT: A 391 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (mp) REVERT: A 420 LYS cc_start: 0.6258 (mttt) cc_final: 0.5718 (mmmm) REVERT: B 194 THR cc_start: 0.9221 (m) cc_final: 0.9013 (m) REVERT: B 352 HIS cc_start: 0.7571 (m-70) cc_final: 0.7290 (t70) REVERT: C 20 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7945 (mm-30) REVERT: C 33 GLU cc_start: 0.8132 (mp0) cc_final: 0.7587 (tp30) REVERT: C 45 ILE cc_start: 0.8828 (mt) cc_final: 0.8560 (mt) REVERT: C 339 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8653 (mt) REVERT: C 347 ASP cc_start: 0.8897 (t70) cc_final: 0.8697 (t0) REVERT: D 19 VAL cc_start: 0.8584 (p) cc_final: 0.8283 (m) REVERT: D 58 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6912 (mpp) REVERT: E 169 THR cc_start: 0.8269 (p) cc_final: 0.8049 (p) REVERT: F 196 MET cc_start: 0.8912 (mtp) cc_final: 0.8607 (mtp) REVERT: F 212 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9001 (mm) REVERT: F 284 ILE cc_start: 0.8850 (pt) cc_final: 0.8607 (mt) REVERT: G 154 GLU cc_start: 0.8627 (pt0) cc_final: 0.8321 (pt0) REVERT: H 29 THR cc_start: 0.7603 (m) cc_final: 0.7336 (p) REVERT: H 32 GLU cc_start: 0.6604 (tp30) cc_final: 0.6186 (tm-30) REVERT: H 70 GLU cc_start: 0.8348 (tp30) cc_final: 0.7884 (tm-30) REVERT: H 93 MET cc_start: 0.6871 (tpp) cc_final: 0.5208 (ttp) REVERT: H 164 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8418 (tpp) REVERT: I 8 MET cc_start: 0.8398 (mmm) cc_final: 0.8122 (mmt) REVERT: I 49 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: I 185 SER cc_start: 0.8388 (m) cc_final: 0.7992 (p) REVERT: I 199 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7983 (mt) REVERT: J 4 GLN cc_start: 0.8213 (mt0) cc_final: 0.7992 (mt0) REVERT: J 125 ASP cc_start: 0.8853 (t0) cc_final: 0.8310 (t0) REVERT: J 189 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8443 (mtmm) REVERT: J 213 ASP cc_start: 0.8280 (m-30) cc_final: 0.8034 (m-30) outliers start: 120 outliers final: 64 residues processed: 503 average time/residue: 0.1537 time to fit residues: 130.0242 Evaluate side-chains 416 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 345 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 199 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 75 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 265 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 397 optimal weight: 30.0000 chunk 14 optimal weight: 0.7980 chunk 379 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS E 347 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 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 = 0.3833 r_free = 0.3833 target = 0.125070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095379 restraints weight = 82469.434| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.68 r_work: 0.3232 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.7898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29032 Z= 0.200 Angle : 0.613 14.702 39465 Z= 0.331 Chirality : 0.046 0.282 4868 Planarity : 0.003 0.053 5057 Dihedral : 5.937 177.973 4130 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 3.87 % Allowed : 17.63 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.11 (0.14), residues: 4046 helix: 1.51 (0.13), residues: 1647 sheet: -1.40 (0.20), residues: 620 loop : -1.06 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 54 TYR 0.023 0.001 TYR A 128 PHE 0.018 0.002 PHE I 121 TRP 0.014 0.001 TRP A 97 HIS 0.009 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00464 (29032) covalent geometry : angle 0.61264 (39465) hydrogen bonds : bond 0.02866 ( 1296) hydrogen bonds : angle 3.78840 ( 3744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 351 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 374 ILE cc_start: 0.8790 (mt) cc_final: 0.8565 (mt) REVERT: A 384 HIS cc_start: 0.7943 (m-70) cc_final: 0.7545 (t70) REVERT: A 391 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 420 LYS cc_start: 0.6424 (mttt) cc_final: 0.5977 (mmmm) REVERT: B 352 HIS cc_start: 0.7593 (m-70) cc_final: 0.7323 (t70) REVERT: C 33 GLU cc_start: 0.8168 (mp0) cc_final: 0.7635 (tp30) REVERT: C 45 ILE cc_start: 0.8796 (mt) cc_final: 0.8562 (mt) REVERT: C 217 MET cc_start: 0.9315 (ptt) cc_final: 0.9111 (ptt) REVERT: C 339 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8619 (mt) REVERT: D 19 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8387 (m) REVERT: D 58 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: F 212 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8981 (mm) REVERT: F 235 GLN cc_start: 0.8415 (tm-30) cc_final: 0.8014 (tm-30) REVERT: G 120 LYS cc_start: 0.7869 (mmpt) cc_final: 0.7665 (mmtm) REVERT: G 154 GLU cc_start: 0.8599 (pt0) cc_final: 0.8350 (pt0) REVERT: G 168 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7843 (mp) REVERT: H 32 GLU cc_start: 0.6739 (tp30) cc_final: 0.6296 (tm-30) REVERT: H 70 GLU cc_start: 0.8258 (tp30) cc_final: 0.7759 (tm-30) REVERT: H 164 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8598 (tpp) REVERT: I 49 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: I 185 SER cc_start: 0.8415 (m) cc_final: 0.8064 (p) REVERT: J 125 ASP cc_start: 0.8831 (t0) cc_final: 0.8314 (t0) REVERT: J 189 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8458 (mtmm) REVERT: J 213 ASP cc_start: 0.8470 (m-30) cc_final: 0.8165 (m-30) REVERT: J 215 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8158 (mp) REVERT: L 130 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7738 (t80) REVERT: S 315 PHE cc_start: 0.7671 (m-80) cc_final: 0.7304 (m-80) outliers start: 100 outliers final: 73 residues processed: 430 average time/residue: 0.1620 time to fit residues: 117.0988 Evaluate side-chains 410 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 215 MET Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 245 ASP Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 323 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 364 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 HIS D 72 GLN E 194 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.123245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092186 restraints weight = 99107.121| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.53 r_work: 0.3200 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.8481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29032 Z= 0.217 Angle : 0.636 14.878 39465 Z= 0.341 Chirality : 0.047 0.202 4868 Planarity : 0.003 0.055 5057 Dihedral : 6.044 177.885 4130 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.72 % Allowed : 18.25 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: -0.10 (0.14), residues: 4046 helix: 1.53 (0.13), residues: 1650 sheet: -1.50 (0.20), residues: 627 loop : -1.03 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 54 TYR 0.026 0.002 TYR A 128 PHE 0.031 0.002 PHE G 33 TRP 0.013 0.001 TRP J 37 HIS 0.008 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00506 (29032) covalent geometry : angle 0.63555 (39465) hydrogen bonds : bond 0.03106 ( 1296) hydrogen bonds : angle 3.87320 ( 3744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 335 time to evaluate : 0.865 Fit side-chains REVERT: A 174 LEU cc_start: 0.8680 (mm) cc_final: 0.8427 (mm) REVERT: A 420 LYS cc_start: 0.6464 (mttt) cc_final: 0.6115 (mmmm) REVERT: B 352 HIS cc_start: 0.7606 (m-70) cc_final: 0.7347 (t70) REVERT: B 373 PHE cc_start: 0.8201 (t80) cc_final: 0.8000 (t80) REVERT: C 33 GLU cc_start: 0.8212 (mp0) cc_final: 0.7749 (tp30) REVERT: C 58 MET cc_start: 0.8635 (mmt) cc_final: 0.8289 (mmt) REVERT: D 16 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 19 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8372 (m) REVERT: D 58 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6503 (mpp) REVERT: F 212 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8995 (mm) REVERT: G 120 LYS cc_start: 0.8027 (mmpt) cc_final: 0.7735 (mmtm) REVERT: G 154 GLU cc_start: 0.8553 (pt0) cc_final: 0.8162 (pt0) REVERT: G 168 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8065 (mp) REVERT: H 32 GLU cc_start: 0.6707 (tp30) cc_final: 0.6437 (tm-30) REVERT: H 70 GLU cc_start: 0.8284 (tp30) cc_final: 0.7826 (tm-30) REVERT: H 164 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8650 (tpp) REVERT: I 2 GLU cc_start: 0.7745 (tt0) cc_final: 0.7335 (pt0) REVERT: I 8 MET cc_start: 0.8599 (mmm) cc_final: 0.8258 (mmt) REVERT: I 185 SER cc_start: 0.8544 (m) cc_final: 0.8161 (p) REVERT: I 203 HIS cc_start: 0.8123 (t-90) cc_final: 0.6917 (m90) REVERT: J 116 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7769 (mp0) REVERT: J 125 ASP cc_start: 0.8836 (t0) cc_final: 0.8341 (t0) REVERT: J 189 LYS cc_start: 0.8806 (mtpp) cc_final: 0.8501 (mtmm) REVERT: J 215 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8283 (mp) REVERT: L 39 ASN cc_start: 0.9332 (t0) cc_final: 0.9104 (t0) REVERT: L 130 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8012 (t80) REVERT: S 315 PHE cc_start: 0.7905 (m-80) cc_final: 0.7651 (m-80) outliers start: 96 outliers final: 71 residues processed: 411 average time/residue: 0.1637 time to fit residues: 112.1755 Evaluate side-chains 395 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 234 optimal weight: 6.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN E 234 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** 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 = 0.3810 r_free = 0.3810 target = 0.123646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.092802 restraints weight = 87232.419| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.61 r_work: 0.3205 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29032 Z= 0.189 Angle : 0.605 15.197 39465 Z= 0.326 Chirality : 0.046 0.207 4868 Planarity : 0.003 0.055 5057 Dihedral : 5.995 179.448 4130 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.29 % Allowed : 18.98 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 0.04 (0.14), residues: 4046 helix: 1.69 (0.13), residues: 1639 sheet: -1.45 (0.20), residues: 619 loop : -0.97 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 52 TYR 0.022 0.001 TYR A 128 PHE 0.020 0.001 PHE G 33 TRP 0.012 0.001 TRP J 37 HIS 0.006 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00439 (29032) covalent geometry : angle 0.60491 (39465) hydrogen bonds : bond 0.02872 ( 1296) hydrogen bonds : angle 3.83751 ( 3744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 341 time to evaluate : 1.156 Fit side-chains REVERT: A 420 LYS cc_start: 0.6580 (mttt) cc_final: 0.6284 (mmmm) REVERT: B 264 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: B 352 HIS cc_start: 0.7704 (m-70) cc_final: 0.7498 (t-90) REVERT: B 373 PHE cc_start: 0.8201 (t80) cc_final: 0.7816 (t80) REVERT: C 13 GLU cc_start: 0.8033 (tp30) cc_final: 0.7762 (tm-30) REVERT: C 33 GLU cc_start: 0.8177 (mp0) cc_final: 0.7720 (tp30) REVERT: C 58 MET cc_start: 0.8672 (mmt) cc_final: 0.8424 (mmt) REVERT: D 16 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7691 (mm-30) REVERT: D 19 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8467 (m) REVERT: D 58 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6963 (mpp) REVERT: F 212 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8979 (mm) REVERT: G 154 GLU cc_start: 0.8566 (pt0) cc_final: 0.8203 (pt0) REVERT: G 168 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8084 (mp) REVERT: H 32 GLU cc_start: 0.6755 (tp30) cc_final: 0.6472 (tm-30) REVERT: H 70 GLU cc_start: 0.8271 (tp30) cc_final: 0.7786 (tm-30) REVERT: I 2 GLU cc_start: 0.7750 (tt0) cc_final: 0.6908 (pt0) REVERT: I 8 MET cc_start: 0.8653 (mmm) cc_final: 0.8362 (mmt) REVERT: I 185 SER cc_start: 0.8589 (m) cc_final: 0.8219 (p) REVERT: I 203 HIS cc_start: 0.8170 (t-90) cc_final: 0.6941 (m90) REVERT: J 125 ASP cc_start: 0.8881 (t0) cc_final: 0.8382 (t0) REVERT: J 189 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8489 (mtmm) REVERT: J 215 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8373 (mp) REVERT: L 39 ASN cc_start: 0.9278 (t0) cc_final: 0.8963 (t0) REVERT: L 130 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8030 (t80) outliers start: 85 outliers final: 73 residues processed: 409 average time/residue: 0.1671 time to fit residues: 113.8795 Evaluate side-chains 407 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 305 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 359 optimal weight: 20.0000 chunk 342 optimal weight: 7.9990 chunk 334 optimal weight: 4.9990 chunk 397 optimal weight: 30.0000 chunk 277 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093468 restraints weight = 89485.260| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.34 r_work: 0.3233 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.8817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29032 Z= 0.162 Angle : 0.591 14.812 39465 Z= 0.317 Chirality : 0.045 0.204 4868 Planarity : 0.003 0.055 5057 Dihedral : 5.911 179.755 4130 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.64 % Allowed : 18.98 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 0.13 (0.14), residues: 4046 helix: 1.75 (0.13), residues: 1642 sheet: -1.40 (0.20), residues: 612 loop : -0.93 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 53 TYR 0.018 0.001 TYR A 128 PHE 0.024 0.001 PHE G 33 TRP 0.011 0.001 TRP J 37 HIS 0.006 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00369 (29032) covalent geometry : angle 0.59082 (39465) hydrogen bonds : bond 0.02731 ( 1296) hydrogen bonds : angle 3.77869 ( 3744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 343 time to evaluate : 1.072 Fit side-chains REVERT: A 420 LYS cc_start: 0.6585 (mttt) cc_final: 0.6321 (mmmm) REVERT: B 264 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: B 352 HIS cc_start: 0.7729 (m-70) cc_final: 0.7449 (t-90) REVERT: B 373 PHE cc_start: 0.8144 (t80) cc_final: 0.7790 (t80) REVERT: C 13 GLU cc_start: 0.8049 (tp30) cc_final: 0.7756 (tm-30) REVERT: C 33 GLU cc_start: 0.8124 (mp0) cc_final: 0.7681 (tp30) REVERT: C 58 MET cc_start: 0.8627 (mmt) cc_final: 0.8427 (mmt) REVERT: C 138 ASN cc_start: 0.9239 (m-40) cc_final: 0.8820 (m110) REVERT: C 305 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8223 (pttt) REVERT: D 16 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 19 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8383 (m) REVERT: D 58 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7015 (mpp) REVERT: D 212 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (mt) REVERT: G 154 GLU cc_start: 0.8494 (pt0) cc_final: 0.8208 (pt0) REVERT: G 168 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8078 (mp) REVERT: H 32 GLU cc_start: 0.6956 (tp30) cc_final: 0.6677 (tm-30) REVERT: H 70 GLU cc_start: 0.8271 (tp30) cc_final: 0.7788 (tm-30) REVERT: I 2 GLU cc_start: 0.7671 (tt0) cc_final: 0.7095 (pt0) REVERT: I 8 MET cc_start: 0.8624 (mmm) cc_final: 0.8319 (mmt) REVERT: I 185 SER cc_start: 0.8568 (m) cc_final: 0.8191 (p) REVERT: I 203 HIS cc_start: 0.8124 (t-90) cc_final: 0.6912 (m90) REVERT: J 116 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7739 (mp0) REVERT: J 125 ASP cc_start: 0.8829 (t0) cc_final: 0.8326 (t0) REVERT: J 156 ASP cc_start: 0.7135 (p0) cc_final: 0.6742 (t0) REVERT: J 189 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8492 (mtmm) REVERT: J 215 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8393 (mp) REVERT: L 25 SER cc_start: 0.9114 (t) cc_final: 0.8752 (p) REVERT: L 39 ASN cc_start: 0.9251 (t0) cc_final: 0.8936 (t0) REVERT: L 130 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8055 (t80) outliers start: 94 outliers final: 73 residues processed: 419 average time/residue: 0.1649 time to fit residues: 114.5911 Evaluate side-chains 412 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 331 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 299 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 152 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 393 optimal weight: 0.0470 chunk 362 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN D 72 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095584 restraints weight = 71370.027| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.92 r_work: 0.3280 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29032 Z= 0.137 Angle : 0.570 15.039 39465 Z= 0.308 Chirality : 0.044 0.210 4868 Planarity : 0.003 0.054 5057 Dihedral : 5.771 177.669 4130 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.67 % Allowed : 19.64 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 0.26 (0.14), residues: 4046 helix: 1.85 (0.13), residues: 1650 sheet: -1.30 (0.21), residues: 622 loop : -0.86 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 54 TYR 0.014 0.001 TYR A 128 PHE 0.023 0.001 PHE G 33 TRP 0.010 0.001 TRP J 37 HIS 0.007 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00296 (29032) covalent geometry : angle 0.57040 (39465) hydrogen bonds : bond 0.02583 ( 1296) hydrogen bonds : angle 3.70533 ( 3744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 347 time to evaluate : 1.015 Fit side-chains REVERT: B 264 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: B 352 HIS cc_start: 0.7682 (m-70) cc_final: 0.7458 (t-90) REVERT: B 373 PHE cc_start: 0.8033 (t80) cc_final: 0.7767 (t80) REVERT: B 433 SER cc_start: 0.8708 (m) cc_final: 0.8298 (p) REVERT: C 13 GLU cc_start: 0.7960 (tp30) cc_final: 0.7730 (tm-30) REVERT: C 33 GLU cc_start: 0.7975 (mp0) cc_final: 0.7627 (tp30) REVERT: C 58 MET cc_start: 0.8567 (mmt) cc_final: 0.8342 (mmt) REVERT: C 138 ASN cc_start: 0.9212 (m-40) cc_final: 0.8813 (m110) REVERT: C 305 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8201 (pttt) REVERT: D 16 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 19 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8451 (m) REVERT: D 58 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7351 (mmt) REVERT: D 212 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8725 (mt) REVERT: G 154 GLU cc_start: 0.8408 (pt0) cc_final: 0.8128 (pt0) REVERT: G 168 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8087 (mp) REVERT: H 32 GLU cc_start: 0.7065 (tp30) cc_final: 0.6765 (tm-30) REVERT: H 70 GLU cc_start: 0.8212 (tp30) cc_final: 0.7789 (tt0) REVERT: H 164 MET cc_start: 0.9088 (tpt) cc_final: 0.8746 (tpt) REVERT: I 2 GLU cc_start: 0.7595 (tt0) cc_final: 0.7171 (pt0) REVERT: I 8 MET cc_start: 0.8563 (mmm) cc_final: 0.8281 (mmt) REVERT: I 185 SER cc_start: 0.8567 (m) cc_final: 0.8190 (p) REVERT: I 203 HIS cc_start: 0.8022 (t-90) cc_final: 0.6909 (m90) REVERT: J 125 ASP cc_start: 0.8760 (t0) cc_final: 0.8150 (t0) REVERT: J 189 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8482 (mtmm) REVERT: L 25 SER cc_start: 0.9079 (t) cc_final: 0.8766 (p) REVERT: L 39 ASN cc_start: 0.9221 (t0) cc_final: 0.8937 (t0) REVERT: L 130 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8036 (t80) outliers start: 69 outliers final: 56 residues processed: 402 average time/residue: 0.1630 time to fit residues: 108.7964 Evaluate side-chains 398 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 244 GLN Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 128 LEU Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 233 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 400 optimal weight: 20.0000 chunk 391 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 HIS C 331 ASN D 72 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091239 restraints weight = 83858.820| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.53 r_work: 0.3156 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.9119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29032 Z= 0.240 Angle : 0.648 13.538 39465 Z= 0.345 Chirality : 0.047 0.211 4868 Planarity : 0.003 0.057 5057 Dihedral : 6.054 179.686 4130 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.98 % Allowed : 19.14 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.79 % 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: 0.13 (0.14), residues: 4046 helix: 1.74 (0.13), residues: 1641 sheet: -1.40 (0.20), residues: 621 loop : -0.90 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 56 TYR 0.026 0.002 TYR A 128 PHE 0.021 0.002 PHE G 33 TRP 0.011 0.001 TRP E 476 HIS 0.005 0.001 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00571 (29032) covalent geometry : angle 0.64757 (39465) hydrogen bonds : bond 0.03033 ( 1296) hydrogen bonds : angle 3.86793 ( 3744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8518.67 seconds wall clock time: 145 minutes 39.36 seconds (8739.36 seconds total)