Starting phenix.real_space_refine on Mon Sep 14 05:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o85_0651/09_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_0651/09_2026/6o85_0651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o85_0651/09_2026/6o85_0651.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.32, 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 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: 0.85 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: 6.96 Time building geometry restraints manager: 3.17 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: 17032 29.64 - 59.28: 306 59.28 - 88.91: 30 88.91 - 118.55: 4 118.55 - 148.19: 2 Dihedral angle restraints: 17374 sinusoidal: 5502 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 17371 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: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.870 Find NCS groups from input model: 0.570 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 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 : 12.435 148.190 9588 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/Z covalent geometry : bond 0.00498 / 0.26 (29032) covalent geometry : angle 0.87052 / 0.51 (39465) hydrogen bonds : bond 0.13948 / 9.08 ( 1296) hydrogen bonds : angle 6.65559 / 4.65 ( 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 : 0.950 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: 0.1554 time to fit residues: 228.5171 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 : 1.040 ------------------------------------------------------------------------------- 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... A 409 HIS B 63 GLN B 72 ASN C 154 GLN C 252 HIS C 261 HIS D 138 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 GLN F 274 HIS F 430 HIS F 479 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4090 r_free = 0.4090 target = 0.145104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.118835 restraints weight = 53630.347| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.59 r_work: 0.3649 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29032 Z= 0.156 Angle : 0.613 11.145 39465 Z= 0.335 Chirality : 0.045 0.161 4868 Planarity : 0.004 0.065 5057 Dihedral : 5.818 169.731 4106 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.41 % Allowed : 13.64 % Favored : 82.95 % 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: -1.94 (0.12), residues: 4046 helix: -0.40 (0.12), residues: 1617 sheet: -1.96 (0.20), residues: 584 loop : -1.80 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 53 TYR 0.026 0.001 TYR H 252 PHE 0.025 0.002 PHE C 177 TRP 0.019 0.002 TRP A 97 HIS 0.008 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (29032) covalent geometry : angle 0.61300 / 0.34 (39465) hydrogen bonds : bond 0.03156 / 2.09 ( 1296) hydrogen bonds : angle 4.26439 / 2.98 ( 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: 88 poor density : 554 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8564 (tp) cc_final: 0.8279 (tp) REVERT: A 394 THR cc_start: 0.8246 (m) cc_final: 0.8030 (p) REVERT: B 224 PHE cc_start: 0.4167 (m-80) cc_final: 0.3766 (m-80) REVERT: B 366 THR cc_start: 0.7036 (t) cc_final: 0.6183 (m) REVERT: C 45 ILE cc_start: 0.8053 (mt) cc_final: 0.7667 (mt) REVERT: E 175 SER cc_start: 0.7355 (t) cc_final: 0.7140 (t) REVERT: E 238 GLN cc_start: 0.8060 (tp40) cc_final: 0.7746 (tt0) REVERT: F 200 SER cc_start: 0.7429 (m) cc_final: 0.6568 (p) REVERT: F 251 ASP cc_start: 0.8512 (t0) cc_final: 0.7947 (t70) REVERT: H 32 GLU cc_start: 0.6310 (tp30) cc_final: 0.5942 (tm-30) REVERT: H 109 ASN cc_start: 0.7350 (m-40) cc_final: 0.6943 (p0) REVERT: H 213 ASN cc_start: 0.8733 (t0) cc_final: 0.8489 (t0) REVERT: I 49 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: J 263 ILE cc_start: 0.7489 (mt) cc_final: 0.7280 (mm) REVERT: L 76 ASP cc_start: 0.7674 (t0) cc_final: 0.7297 (t0) REVERT: L 82 ILE cc_start: 0.8297 (mt) cc_final: 0.8048 (mt) outliers start: 88 outliers final: 54 residues processed: 615 average time/residue: 0.1479 time to fit residues: 153.9916 Evaluate side-chains 514 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 459 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 144 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 242 THR Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 341 LEU 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 238 GLN Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 411 ASN Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 437 CYS 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: 9.9990 chunk 378 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 345 HIS E 347 GLN E 430 HIS E 431 ASN F 254 ASN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS L 40 ASN L 67 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.138665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109926 restraints weight = 83958.568| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.76 r_work: 0.3515 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29032 Z= 0.172 Angle : 0.624 13.580 39465 Z= 0.339 Chirality : 0.046 0.229 4868 Planarity : 0.004 0.054 5057 Dihedral : 5.636 170.407 4102 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.91 % Favored : 96.07 % Rotamer: Outliers : 3.87 % Allowed : 15.30 % Favored : 80.82 % 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: -0.97 (0.13), residues: 4046 helix: 0.62 (0.13), residues: 1624 sheet: -1.66 (0.21), residues: 589 loop : -1.41 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 52 TYR 0.015 0.001 TYR A 128 PHE 0.028 0.002 PHE H 100 TRP 0.011 0.001 TRP J 37 HIS 0.006 0.001 HIS G 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (29032) covalent geometry : angle 0.62371 / 0.34 (39465) hydrogen bonds : bond 0.03083 / 2.06 ( 1296) hydrogen bonds : angle 3.85742 / 2.70 ( 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 598 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 498 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: B 307 SER cc_start: 0.9030 (m) cc_final: 0.8699 (p) REVERT: B 352 HIS cc_start: 0.7005 (m-70) cc_final: 0.6716 (t70) REVERT: C 45 ILE cc_start: 0.8299 (mt) cc_final: 0.7931 (mt) REVERT: C 226 MET cc_start: 0.8793 (tpt) cc_final: 0.8468 (tpt) REVERT: D 58 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6718 (mpp) REVERT: E 175 SER cc_start: 0.8061 (t) cc_final: 0.7847 (t) REVERT: E 238 GLN cc_start: 0.8456 (tp40) cc_final: 0.8233 (tt0) REVERT: F 200 SER cc_start: 0.7810 (m) cc_final: 0.7065 (p) REVERT: F 251 ASP cc_start: 0.8659 (t0) cc_final: 0.8090 (t70) REVERT: H 20 MET cc_start: 0.6663 (tpp) cc_final: 0.6291 (ttm) REVERT: H 32 GLU cc_start: 0.6378 (tp30) cc_final: 0.5942 (tm-30) REVERT: H 93 MET cc_start: 0.6715 (tpp) cc_final: 0.4824 (ttp) REVERT: H 109 ASN cc_start: 0.7683 (m-40) cc_final: 0.7204 (p0) REVERT: H 202 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8434 (tm-30) REVERT: H 245 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6137 (t0) REVERT: I 49 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: J 50 GLU cc_start: 0.8775 (pt0) cc_final: 0.8565 (tm-30) REVERT: L 76 ASP cc_start: 0.7996 (t0) cc_final: 0.7753 (t0) REVERT: L 111 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7530 (tt) outliers start: 100 outliers final: 61 residues processed: 567 average time/residue: 0.1524 time to fit residues: 145.4603 Evaluate side-chains 479 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 414 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 342 ILE 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 202 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 C residue 144 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 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 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 293 GLU 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 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 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 183 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 183 LYS 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: 40.0000 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 326 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 170 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 130 GLN C 201 HIS E 254 ASN E 431 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099851 restraints weight = 77374.842| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.19 r_work: 0.3311 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.7288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 29032 Z= 0.280 Angle : 0.735 13.753 39465 Z= 0.395 Chirality : 0.050 0.209 4868 Planarity : 0.004 0.052 5057 Dihedral : 5.980 162.887 4102 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.49 % Allowed : 16.62 % Favored : 78.88 % 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: -0.75 (0.13), residues: 4046 helix: 0.85 (0.13), residues: 1629 sheet: -1.51 (0.21), residues: 595 loop : -1.36 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 52 TYR 0.031 0.002 TYR A 128 PHE 0.034 0.002 PHE I 121 TRP 0.018 0.002 TRP J 37 HIS 0.009 0.002 HIS D 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (29032) covalent geometry : angle 0.73521 / 0.40 (39465) hydrogen bonds : bond 0.03485 / 2.31 ( 1296) hydrogen bonds : angle 4.08994 / 2.86 ( 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 515 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 399 time to evaluate : 1.032 Fit side-chains REVERT: A 391 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 420 LYS cc_start: 0.6304 (mttt) cc_final: 0.6070 (mmmm) REVERT: B 352 HIS cc_start: 0.7610 (m-70) cc_final: 0.7391 (t-90) REVERT: C 33 GLU cc_start: 0.8030 (mp0) cc_final: 0.7538 (tp30) REVERT: C 58 MET cc_start: 0.8474 (mmt) cc_final: 0.8077 (mmt) REVERT: C 226 MET cc_start: 0.9192 (tpt) cc_final: 0.8899 (tpt) REVERT: D 19 VAL cc_start: 0.8644 (p) cc_final: 0.8363 (m) REVERT: D 132 ASN cc_start: 0.7783 (m-40) cc_final: 0.7582 (m-40) REVERT: F 212 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9013 (mm) REVERT: G 154 GLU cc_start: 0.8567 (pt0) cc_final: 0.8241 (pt0) REVERT: H 29 THR cc_start: 0.7692 (m) cc_final: 0.7434 (p) REVERT: H 32 GLU cc_start: 0.6748 (tp30) cc_final: 0.6361 (tm-30) REVERT: H 70 GLU cc_start: 0.8388 (tp30) cc_final: 0.7952 (tm-30) REVERT: H 164 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8101 (tpp) REVERT: I 8 MET cc_start: 0.8529 (mmm) cc_final: 0.8177 (mmt) REVERT: I 49 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: I 203 HIS cc_start: 0.8134 (t-90) cc_final: 0.6894 (m90) REVERT: J 125 ASP cc_start: 0.8591 (t0) cc_final: 0.8319 (t0) REVERT: J 189 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8446 (mtmm) REVERT: J 213 ASP cc_start: 0.8202 (m-30) cc_final: 0.7988 (m-30) REVERT: L 86 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8078 (tptt) REVERT: S 315 PHE cc_start: 0.7635 (m-80) cc_final: 0.7150 (m-80) outliers start: 116 outliers final: 59 residues processed: 489 average time/residue: 0.1523 time to fit residues: 124.1218 Evaluate side-chains 401 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE 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 375 THR Chi-restraints excluded: chain A residue 391 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 198 GLU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 91 GLU 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 141 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 117 THR 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 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 J residue 40 LEU 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 186 ILE Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 75 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 150 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 294 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 422 GLN H 116 HIS L 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099330 restraints weight = 83286.303| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.68 r_work: 0.3284 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29032 Z= 0.143 Angle : 0.570 14.909 39465 Z= 0.312 Chirality : 0.045 0.206 4868 Planarity : 0.003 0.051 5057 Dihedral : 5.638 167.376 4102 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.29 % Allowed : 17.98 % Favored : 78.73 % 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: -0.27 (0.14), residues: 4046 helix: 1.39 (0.13), residues: 1637 sheet: -1.46 (0.21), residues: 613 loop : -1.17 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 53 TYR 0.015 0.001 TYR A 128 PHE 0.019 0.001 PHE I 121 TRP 0.012 0.001 TRP J 37 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (29032) covalent geometry : angle 0.57025 / 0.31 (39465) hydrogen bonds : bond 0.02692 / 1.79 ( 1296) hydrogen bonds : angle 3.74365 / 2.62 ( 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 461 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 376 time to evaluate : 1.057 Fit side-chains REVERT: A 374 ILE cc_start: 0.8704 (mt) cc_final: 0.8493 (mt) REVERT: A 420 LYS cc_start: 0.6243 (mttt) cc_final: 0.5903 (mmmm) REVERT: C 20 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7811 (mm-30) REVERT: C 33 GLU cc_start: 0.8088 (mp0) cc_final: 0.7530 (tp30) REVERT: C 45 ILE cc_start: 0.8668 (mt) cc_final: 0.8279 (mt) REVERT: C 58 MET cc_start: 0.8368 (mmt) cc_final: 0.7989 (mmt) REVERT: C 226 MET cc_start: 0.9169 (tpt) cc_final: 0.8860 (tpt) REVERT: D 19 VAL cc_start: 0.8597 (p) cc_final: 0.8291 (m) REVERT: D 58 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6472 (mpp) REVERT: D 212 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8498 (mm) REVERT: F 284 ILE cc_start: 0.8844 (pt) cc_final: 0.8629 (mt) REVERT: H 29 THR cc_start: 0.7558 (m) cc_final: 0.7283 (p) REVERT: H 32 GLU cc_start: 0.6696 (tp30) cc_final: 0.6285 (tm-30) REVERT: H 70 GLU cc_start: 0.8345 (tp30) cc_final: 0.7860 (tm-30) REVERT: I 8 MET cc_start: 0.8522 (mmm) cc_final: 0.8319 (mmm) REVERT: I 49 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: I 185 SER cc_start: 0.8244 (m) cc_final: 0.7876 (p) REVERT: J 125 ASP cc_start: 0.8651 (t0) cc_final: 0.8371 (t0) REVERT: J 189 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8446 (mtmm) REVERT: J 213 ASP cc_start: 0.8319 (m-30) cc_final: 0.8047 (m-30) REVERT: L 86 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8453 (tttt) REVERT: L 130 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7895 (t80) REVERT: S 315 PHE cc_start: 0.7540 (m-80) cc_final: 0.7165 (m-80) outliers start: 85 outliers final: 50 residues processed: 442 average time/residue: 0.1608 time to fit residues: 118.8722 Evaluate side-chains 401 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 347 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 125 SER 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 C residue 245 LEU Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 189 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 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 175 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU 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 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 177 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 98 LYS Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain L residue 130 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 265 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 284 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 397 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 379 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS B 409 HIS C 331 ASN E 194 GLN E 422 GLN F 204 HIS F 245 ASN H 13 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094037 restraints weight = 93028.152| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.76 r_work: 0.3203 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29032 Z= 0.191 Angle : 0.605 14.647 39465 Z= 0.329 Chirality : 0.046 0.222 4868 Planarity : 0.003 0.053 5057 Dihedral : 5.731 168.922 4102 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.45 % Allowed : 17.90 % Favored : 78.65 % 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: -0.12 (0.14), residues: 4046 helix: 1.52 (0.13), residues: 1662 sheet: -1.37 (0.21), residues: 608 loop : -1.13 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 54 TYR 0.020 0.001 TYR A 128 PHE 0.030 0.002 PHE G 33 TRP 0.013 0.001 TRP J 37 HIS 0.006 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (29032) covalent geometry : angle 0.60532 / 0.33 (39465) hydrogen bonds : bond 0.02896 / 1.92 ( 1296) hydrogen bonds : angle 3.77306 / 2.65 ( 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 440 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 1.023 Fit side-chains REVERT: A 374 ILE cc_start: 0.8859 (mt) cc_final: 0.8625 (mt) REVERT: A 384 HIS cc_start: 0.8034 (m-70) cc_final: 0.7546 (t-90) REVERT: A 420 LYS cc_start: 0.6411 (mttt) cc_final: 0.6075 (mmmm) REVERT: B 51 SER cc_start: 0.7951 (t) cc_final: 0.7715 (p) REVERT: B 352 HIS cc_start: 0.7612 (m-70) cc_final: 0.7309 (t70) REVERT: B 373 PHE cc_start: 0.8137 (t80) cc_final: 0.7714 (t80) REVERT: C 13 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8102 (tp30) REVERT: C 33 GLU cc_start: 0.8209 (mp0) cc_final: 0.7671 (tp30) REVERT: C 58 MET cc_start: 0.8623 (mmt) cc_final: 0.8157 (mmt) REVERT: C 68 MET cc_start: 0.7976 (mtm) cc_final: 0.7350 (mtp) REVERT: C 226 MET cc_start: 0.9290 (tpt) cc_final: 0.8813 (tpt) REVERT: D 19 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8327 (m) REVERT: D 58 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6546 (mpp) REVERT: G 120 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7796 (mttm) REVERT: G 154 GLU cc_start: 0.8629 (pt0) cc_final: 0.8272 (pt0) REVERT: G 168 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7880 (mp) REVERT: H 32 GLU cc_start: 0.6674 (tp30) cc_final: 0.6319 (tm-30) REVERT: H 70 GLU cc_start: 0.8321 (tp30) cc_final: 0.7849 (tm-30) REVERT: H 164 MET cc_start: 0.8957 (tpp) cc_final: 0.8675 (tpp) REVERT: I 49 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: I 185 SER cc_start: 0.8487 (m) cc_final: 0.8098 (p) REVERT: J 125 ASP cc_start: 0.8797 (t0) cc_final: 0.8529 (t0) REVERT: J 189 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8504 (mtmm) REVERT: L 130 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7891 (t80) REVERT: S 315 PHE cc_start: 0.7684 (m-80) cc_final: 0.7433 (m-80) outliers start: 89 outliers final: 63 residues processed: 425 average time/residue: 0.1566 time to fit residues: 111.4094 Evaluate side-chains 397 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 328 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU 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 47 LEU 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 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 419 VAL Chi-restraints excluded: chain B residue 424 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 58 MET Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 189 VAL 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 298 SER 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 269 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 120 LYS 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 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 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 161 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE 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: 4.9990 chunk 364 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 290 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN D 72 GLN G 203 ASN H 156 GLN ** H 208 ASN ** 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 = 0.3841 r_free = 0.3841 target = 0.125666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094749 restraints weight = 101738.915| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.70 r_work: 0.3238 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.8266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29032 Z= 0.156 Angle : 0.568 14.935 39465 Z= 0.310 Chirality : 0.045 0.214 4868 Planarity : 0.003 0.052 5057 Dihedral : 5.622 170.705 4102 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.10 % Allowed : 18.75 % Favored : 78.15 % 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: 0.07 (0.14), residues: 4046 helix: 1.71 (0.13), residues: 1656 sheet: -1.29 (0.21), residues: 613 loop : -1.05 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.017 0.001 TYR A 128 PHE 0.020 0.001 PHE G 33 TRP 0.011 0.001 TRP J 37 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (29032) covalent geometry : angle 0.56792 / 0.31 (39465) hydrogen bonds : bond 0.02684 / 1.78 ( 1296) hydrogen bonds : angle 3.69028 / 2.59 ( 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 437 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8691 (mm) cc_final: 0.8455 (mm) REVERT: A 374 ILE cc_start: 0.8884 (mt) cc_final: 0.8656 (mt) REVERT: A 384 HIS cc_start: 0.7969 (m-70) cc_final: 0.7624 (t-90) REVERT: A 420 LYS cc_start: 0.6338 (mttt) cc_final: 0.6130 (mmmm) REVERT: B 51 SER cc_start: 0.8026 (t) cc_final: 0.7781 (p) REVERT: B 352 HIS cc_start: 0.7589 (m-70) cc_final: 0.7373 (t70) REVERT: B 373 PHE cc_start: 0.8131 (t80) cc_final: 0.7786 (t80) REVERT: C 33 GLU cc_start: 0.8132 (mp0) cc_final: 0.7698 (tp30) REVERT: C 138 ASN cc_start: 0.9240 (m-40) cc_final: 0.8851 (m110) REVERT: C 226 MET cc_start: 0.9245 (tpt) cc_final: 0.8760 (tpt) REVERT: C 305 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8148 (pttt) REVERT: D 16 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7659 (mm-30) REVERT: D 19 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8450 (m) REVERT: D 58 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6409 (mpp) REVERT: D 212 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8722 (mt) REVERT: G 154 GLU cc_start: 0.8546 (pt0) cc_final: 0.8316 (pt0) REVERT: G 168 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7836 (mp) REVERT: H 32 GLU cc_start: 0.6653 (tp30) cc_final: 0.6395 (tm-30) REVERT: H 70 GLU cc_start: 0.8272 (tp30) cc_final: 0.7784 (tm-30) REVERT: I 8 MET cc_start: 0.8629 (mmm) cc_final: 0.8346 (mmt) REVERT: I 49 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: I 185 SER cc_start: 0.8531 (m) cc_final: 0.8143 (p) REVERT: J 125 ASP cc_start: 0.8740 (t0) cc_final: 0.8243 (t0) REVERT: J 189 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8518 (mtmm) REVERT: L 39 ASN cc_start: 0.9320 (t0) cc_final: 0.9070 (t0) REVERT: L 86 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8399 (tptt) REVERT: L 130 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7835 (t80) outliers start: 80 outliers final: 61 residues processed: 421 average time/residue: 0.1636 time to fit residues: 114.9690 Evaluate side-chains 403 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 335 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 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 42 LEU Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 189 VAL 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 231 LYS 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 175 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 75 PHE 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 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 161 ASP Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 186 ILE 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: 1.9990 chunk 69 optimal weight: 1.9990 chunk 376 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 337 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094601 restraints weight = 89466.009| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.58 r_work: 0.3248 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.8467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29032 Z= 0.149 Angle : 0.572 14.961 39465 Z= 0.310 Chirality : 0.045 0.200 4868 Planarity : 0.003 0.053 5057 Dihedral : 5.590 172.969 4102 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.02 % Allowed : 18.91 % Favored : 78.07 % 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: 0.21 (0.14), residues: 4046 helix: 1.85 (0.13), residues: 1653 sheet: -1.25 (0.21), residues: 618 loop : -0.96 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 52 TYR 0.015 0.001 TYR A 128 PHE 0.022 0.001 PHE G 33 TRP 0.010 0.001 TRP J 37 HIS 0.004 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (29032) covalent geometry : angle 0.57170 / 0.31 (39465) hydrogen bonds : bond 0.02625 / 1.73 ( 1296) hydrogen bonds : angle 3.65058 / 2.56 ( 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 431 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 353 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 ILE cc_start: 0.8893 (mt) cc_final: 0.8681 (mt) REVERT: A 420 LYS cc_start: 0.6372 (mttt) cc_final: 0.6168 (mmmm) REVERT: B 51 SER cc_start: 0.7894 (t) cc_final: 0.7669 (p) REVERT: B 373 PHE cc_start: 0.8101 (t80) cc_final: 0.7777 (t80) REVERT: B 433 SER cc_start: 0.8782 (m) cc_final: 0.8361 (p) REVERT: C 33 GLU cc_start: 0.8005 (mp0) cc_final: 0.7512 (tp30) REVERT: C 58 MET cc_start: 0.8650 (mmt) cc_final: 0.8127 (mmt) REVERT: C 138 ASN cc_start: 0.9243 (m-40) cc_final: 0.8832 (m110) REVERT: C 226 MET cc_start: 0.9252 (tpt) cc_final: 0.8782 (tpt) REVERT: C 305 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8161 (pttt) REVERT: D 16 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 19 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (m) REVERT: D 58 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6861 (mpp) REVERT: D 212 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8733 (mt) REVERT: G 154 GLU cc_start: 0.8533 (pt0) cc_final: 0.8297 (pt0) REVERT: G 168 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.7917 (mp) REVERT: H 32 GLU cc_start: 0.6707 (tp30) cc_final: 0.6439 (tm-30) REVERT: H 70 GLU cc_start: 0.8269 (tp30) cc_final: 0.7772 (tm-30) REVERT: H 188 GLU cc_start: 0.8880 (pt0) cc_final: 0.8546 (pt0) REVERT: I 8 MET cc_start: 0.8618 (mmm) cc_final: 0.8290 (mmt) REVERT: I 185 SER cc_start: 0.8539 (m) cc_final: 0.8133 (p) REVERT: J 125 ASP cc_start: 0.8778 (t0) cc_final: 0.8466 (t0) REVERT: J 189 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8487 (mtmm) REVERT: L 39 ASN cc_start: 0.9308 (t0) cc_final: 0.9044 (t0) REVERT: L 86 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8390 (tptt) REVERT: L 130 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.7804 (t80) REVERT: S 315 PHE cc_start: 0.7741 (m-80) cc_final: 0.7514 (m-80) outliers start: 78 outliers final: 62 residues processed: 419 average time/residue: 0.1653 time to fit residues: 115.8641 Evaluate side-chains 399 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 331 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 C residue 219 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 305 LYS 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 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 212 ILE Chi-restraints excluded: chain D residue 231 LYS 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 175 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 75 PHE 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 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 J residue 1 MET Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 25 SER 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: 9.9990 chunk 185 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 346 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 342 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 397 optimal weight: 30.0000 chunk 277 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.125215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094489 restraints weight = 97349.011| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.75 r_work: 0.3237 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.8560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29032 Z= 0.145 Angle : 0.569 15.846 39465 Z= 0.308 Chirality : 0.044 0.230 4868 Planarity : 0.003 0.050 5057 Dihedral : 5.569 174.198 4102 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.02 % Allowed : 18.79 % Favored : 78.19 % 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: 0.28 (0.14), residues: 4046 helix: 1.89 (0.13), residues: 1652 sheet: -1.18 (0.21), residues: 608 loop : -0.93 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.014 0.001 TYR A 128 PHE 0.021 0.001 PHE G 33 TRP 0.009 0.001 TRP J 37 HIS 0.004 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (29032) covalent geometry : angle 0.56932 / 0.31 (39465) hydrogen bonds : bond 0.02553 / 1.69 ( 1296) hydrogen bonds : angle 3.63154 / 2.55 ( 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 419 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 341 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 51 SER cc_start: 0.7977 (t) cc_final: 0.7716 (p) REVERT: B 264 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: B 373 PHE cc_start: 0.8155 (t80) cc_final: 0.7829 (t80) REVERT: B 433 SER cc_start: 0.8841 (m) cc_final: 0.8314 (p) REVERT: C 33 GLU cc_start: 0.8048 (mp0) cc_final: 0.7593 (tp30) REVERT: C 68 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7879 (mtt) REVERT: C 138 ASN cc_start: 0.9269 (m-40) cc_final: 0.8866 (m110) REVERT: C 226 MET cc_start: 0.9226 (tpt) cc_final: 0.8860 (tpt) REVERT: C 305 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8214 (pttt) REVERT: D 16 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7697 (mm-30) REVERT: D 19 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8450 (m) REVERT: D 58 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6754 (mpp) REVERT: G 120 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7754 (mttm) REVERT: G 154 GLU cc_start: 0.8539 (pt0) cc_final: 0.8312 (pt0) REVERT: G 168 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7928 (mp) REVERT: H 32 GLU cc_start: 0.6805 (tp30) cc_final: 0.6525 (tm-30) REVERT: H 70 GLU cc_start: 0.8240 (tp30) cc_final: 0.7744 (tm-30) REVERT: I 8 MET cc_start: 0.8611 (mmm) cc_final: 0.8318 (mmt) REVERT: I 185 SER cc_start: 0.8587 (m) cc_final: 0.8188 (p) REVERT: J 125 ASP cc_start: 0.8813 (t0) cc_final: 0.8496 (t0) REVERT: J 189 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8487 (mtmm) REVERT: L 39 ASN cc_start: 0.9304 (t0) cc_final: 0.9067 (t0) REVERT: L 86 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8386 (tptt) REVERT: L 130 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7895 (t80) REVERT: S 315 PHE cc_start: 0.7773 (m-80) cc_final: 0.7529 (m-80) outliers start: 78 outliers final: 61 residues processed: 405 average time/residue: 0.1679 time to fit residues: 112.6076 Evaluate side-chains 402 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 333 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 302 ASN 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 68 MET Chi-restraints excluded: chain C residue 219 ASP 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 274 LEU Chi-restraints excluded: chain C residue 305 LYS 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 231 LYS 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 175 SER Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 120 LYS 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 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 J residue 1 MET Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 25 SER 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: 0.7980 chunk 256 optimal weight: 0.2980 chunk 222 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 393 optimal weight: 9.9990 chunk 362 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 chunk 348 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 422 GLN H 156 GLN ** 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 = 0.123195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092647 restraints weight = 92390.292| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.53 r_work: 0.3207 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.8839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29032 Z= 0.188 Angle : 0.610 16.095 39465 Z= 0.327 Chirality : 0.046 0.233 4868 Planarity : 0.003 0.053 5057 Dihedral : 5.695 173.351 4102 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.94 % Allowed : 19.06 % Favored : 77.99 % 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: 0.20 (0.14), residues: 4046 helix: 1.78 (0.13), residues: 1655 sheet: -1.29 (0.21), residues: 622 loop : -0.90 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 53 TYR 0.020 0.001 TYR A 128 PHE 0.020 0.001 PHE G 33 TRP 0.010 0.001 TRP I 37 HIS 0.004 0.001 HIS B 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (29032) covalent geometry : angle 0.60987 / 0.33 (39465) hydrogen bonds : bond 0.02837 / 1.87 ( 1296) hydrogen bonds : angle 3.75420 / 2.63 ( 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 405 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 329 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8563 (m-80) REVERT: B 433 SER cc_start: 0.8866 (m) cc_final: 0.8414 (p) REVERT: C 33 GLU cc_start: 0.8101 (mp0) cc_final: 0.7681 (tp30) REVERT: C 68 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: C 226 MET cc_start: 0.9287 (tpt) cc_final: 0.8739 (tpt) REVERT: C 305 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8242 (pttt) REVERT: D 16 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7734 (mm-30) REVERT: D 19 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8438 (m) REVERT: G 120 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7788 (mttm) REVERT: G 154 GLU cc_start: 0.8558 (pt0) cc_final: 0.8318 (pt0) REVERT: G 168 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8121 (mp) REVERT: H 32 GLU cc_start: 0.6910 (tp30) cc_final: 0.6638 (tm-30) REVERT: H 70 GLU cc_start: 0.8256 (tp30) cc_final: 0.7815 (tt0) REVERT: H 164 MET cc_start: 0.9163 (tpt) cc_final: 0.8822 (tpt) REVERT: I 8 MET cc_start: 0.8646 (mmm) cc_final: 0.8310 (mmt) REVERT: I 185 SER cc_start: 0.8611 (m) cc_final: 0.8226 (p) REVERT: I 203 HIS cc_start: 0.8104 (t-90) cc_final: 0.6976 (m90) REVERT: J 125 ASP cc_start: 0.8849 (t0) cc_final: 0.8537 (t0) REVERT: J 189 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8500 (mtmm) REVERT: L 39 ASN cc_start: 0.9262 (t0) cc_final: 0.8961 (t0) REVERT: L 86 LYS cc_start: 0.9019 (ttmm) cc_final: 0.8409 (tptt) REVERT: L 130 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8042 (t80) REVERT: S 315 PHE cc_start: 0.7927 (m-80) cc_final: 0.7703 (m-80) outliers start: 76 outliers final: 66 residues processed: 391 average time/residue: 0.1660 time to fit residues: 108.1089 Evaluate side-chains 396 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 47 LEU 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 289 MET Chi-restraints excluded: chain B residue 302 ASN 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 68 MET Chi-restraints excluded: chain C residue 219 ASP 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 274 LEU Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 42 LEU 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 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 269 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 120 LYS 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 246 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain H residue 99 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 1 MET Chi-restraints excluded: chain J residue 109 ILE Chi-restraints excluded: chain J residue 127 SER Chi-restraints excluded: chain J residue 183 LYS Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain L residue 25 SER 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 386 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 400 optimal weight: 8.9990 chunk 391 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 72 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.122810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092492 restraints weight = 91423.830| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.32 r_work: 0.3249 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29032 Z= 0.170 Angle : 0.593 15.717 39465 Z= 0.319 Chirality : 0.045 0.234 4868 Planarity : 0.003 0.052 5057 Dihedral : 5.677 175.858 4102 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.91 % Allowed : 19.33 % Favored : 77.76 % 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: 0.25 (0.14), residues: 4046 helix: 1.84 (0.13), residues: 1649 sheet: -1.25 (0.21), residues: 604 loop : -0.89 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 53 TYR 0.017 0.001 TYR A 128 PHE 0.020 0.001 PHE G 33 TRP 0.010 0.001 TRP J 37 HIS 0.004 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (29032) covalent geometry : angle 0.59327 / 0.32 (39465) hydrogen bonds : bond 0.02731 / 1.80 ( 1296) hydrogen bonds : angle 3.72499 / 2.61 ( 3744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8298.23 seconds wall clock time: 142 minutes 12.23 seconds (8532.23 seconds total)