Starting phenix.real_space_refine on Fri Mar 6 11:31:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.map" model { file = "/net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ybd_10769/03_2026/6ybd_10769.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 19177 2.51 5 N 5699 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30742 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 1917 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 263} Link IDs: {'PTRANS': 6, 'TRANS': 343} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 914 Unresolved non-hydrogen angles: 1159 Unresolved non-hydrogen dihedrals: 747 Unresolved non-hydrogen chiralities: 90 Planarities with less than four sites: {'GLU:plan': 27, 'ASP:plan': 20, 'GLN:plan1': 12, 'ARG:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 11, 'HIS:plan': 7, 'PHE:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 473 Chain: "4" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1272 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 993 Unresolved non-hydrogen dihedrals: 618 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'ARG:plan': 11, 'HIS:plan': 8, 'ASP:plan': 14, 'TYR:plan': 11, 'GLU:plan': 15, 'ASN:plan1': 16, 'PHE:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 399 Chain: "u" Number of atoms: 4708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 572, 4700 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} Conformer: "B" Number of residues, atoms: 572, 4700 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 24, 'TRANS': 547} bond proxies already assigned to first conformer: 4780 Chain: "v" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2635 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 10, 'TRANS': 373} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 13, 'GLN:plan1': 9, 'ASP:plan': 15, 'PHE:plan': 7, 'TYR:plan': 10, 'HIS:plan': 2, 'ARG:plan': 9, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 342 Chain: "y" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4325 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "8" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1571 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 285} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1332 Unresolved non-hydrogen dihedrals: 868 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASP:plan': 16, 'GLN:plan1': 31, 'HIS:plan': 10, 'TYR:plan': 14, 'GLU:plan': 24, 'ARG:plan': 12, 'ASN:plan1': 14, 'PHE:plan': 10, 'TRP:plan': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 599 Chain: "G" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1430 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 2 Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 631 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "K" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 617 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 432 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1707 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "O" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1633 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 792 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain: "P" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 997 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "x" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 514 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain breaks: 1 Chain: "3" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 904 Unresolved non-hydrogen dihedrals: 590 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'PHE:plan': 11, 'GLU:plan': 17, 'GLN:plan1': 14, 'ARG:plan': 7, 'ASN:plan1': 9, 'ASP:plan': 14, 'TYR:plan': 7, 'HIS:plan': 5, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 404 Chain: "5" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 1581 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 289} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1124 Unresolved non-hydrogen angles: 1435 Unresolved non-hydrogen dihedrals: 958 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'TRP:plan': 3, 'ASP:plan': 18, 'GLU:plan': 21, 'PHE:plan': 18, 'TYR:plan': 21, 'GLN:plan1': 20, 'ARG:plan': 14, 'ASN:plan1': 11, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 653 Time building chain proxies: 7.56, per 1000 atoms: 0.25 Number of scatterers: 30742 At special positions: 0 Unit cell: (213.726, 214.8, 187.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5736 8.00 N 5699 7.00 C 19177 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: 2.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8454 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 36 sheets defined 49.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain '6' and resid 17 through 25 Processing helix chain '6' and resid 30 through 35 Processing helix chain '6' and resid 63 through 68 removed outlier: 4.147A pdb=" N VAL 6 68 " --> pdb=" O MET 6 64 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 92 removed outlier: 3.777A pdb=" N LEU 6 90 " --> pdb=" O CYS 6 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS 6 92 " --> pdb=" O LYS 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 106 removed outlier: 3.604A pdb=" N ARG 6 102 " --> pdb=" O ARG 6 98 " (cutoff:3.500A) Processing helix chain '6' and resid 107 through 109 No H-bonds generated for 'chain '6' and resid 107 through 109' Processing helix chain '6' and resid 116 through 128 Processing helix chain '6' and resid 154 through 168 Processing helix chain '6' and resid 174 through 193 Processing helix chain '6' and resid 198 through 212 removed outlier: 3.881A pdb=" N VAL 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) Processing helix chain '6' and resid 262 through 267 removed outlier: 3.532A pdb=" N LEU 6 266 " --> pdb=" O PHE 6 262 " (cutoff:3.500A) Processing helix chain '6' and resid 268 through 278 Processing helix chain '6' and resid 280 through 285 Processing helix chain '6' and resid 296 through 301 Processing helix chain '6' and resid 307 through 318 removed outlier: 4.841A pdb=" N ILE 6 313 " --> pdb=" O GLU 6 309 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP 6 314 " --> pdb=" O ALA 6 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR 6 318 " --> pdb=" O ASP 6 314 " (cutoff:3.500A) Processing helix chain '6' and resid 341 through 346 Processing helix chain '6' and resid 347 through 355 removed outlier: 3.763A pdb=" N TYR 6 351 " --> pdb=" O TRP 6 347 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 106 Processing helix chain '4' and resid 152 through 163 Processing helix chain '4' and resid 183 through 192 Processing helix chain '4' and resid 245 through 254 Processing helix chain '4' and resid 266 through 290 Processing helix chain '4' and resid 295 through 298 No H-bonds generated for 'chain '4' and resid 295 through 298' Processing helix chain '4' and resid 304 through 314 removed outlier: 4.269A pdb=" N LEU 4 308 " --> pdb=" O VAL 4 304 " (cutoff:3.500A) Processing helix chain '4' and resid 320 through 352 Processing helix chain 'u' and resid 8 through 16 removed outlier: 4.124A pdb=" N LEU u 12 " --> pdb=" O PRO u 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS u 13 " --> pdb=" O GLU u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 23 through 36 removed outlier: 3.780A pdb=" N LEU u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 46 through 61 Processing helix chain 'u' and resid 64 through 77 Processing helix chain 'u' and resid 83 through 103 Processing helix chain 'u' and resid 105 through 116 removed outlier: 3.615A pdb=" N MET u 111 " --> pdb=" O GLU u 107 " (cutoff:3.500A) Processing helix chain 'u' and resid 128 through 132 Processing helix chain 'u' and resid 139 through 144 removed outlier: 3.993A pdb=" N ARG u 143 " --> pdb=" O ASP u 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU u 144 " --> pdb=" O ARG u 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 139 through 144' Processing helix chain 'u' and resid 146 through 163 removed outlier: 3.569A pdb=" N LEU u 161 " --> pdb=" O TYR u 157 " (cutoff:3.500A) Processing helix chain 'u' and resid 170 through 188 removed outlier: 3.656A pdb=" N HIS u 175 " --> pdb=" O GLU u 171 " (cutoff:3.500A) Processing helix chain 'u' and resid 191 through 204 removed outlier: 4.432A pdb=" N ARG u 195 " --> pdb=" O LYS u 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS u 196 " --> pdb=" O ALA u 192 " (cutoff:3.500A) Processing helix chain 'u' and resid 207 through 211 Processing helix chain 'u' and resid 222 through 242 removed outlier: 3.713A pdb=" N GLU u 231 " --> pdb=" O SER u 227 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR u 232 " --> pdb=" O MET u 228 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG u 233 " --> pdb=" O HIS u 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER u 242 " --> pdb=" O ASP u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 247 through 260 Processing helix chain 'u' and resid 271 through 286 removed outlier: 3.648A pdb=" N ASN u 277 " --> pdb=" O ALA u 273 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER u 280 " --> pdb=" O TYR u 276 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR u 281 " --> pdb=" O ASN u 277 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP u 284 " --> pdb=" O SER u 280 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS u 285 " --> pdb=" O THR u 281 " (cutoff:3.500A) Processing helix chain 'u' and resid 288 through 307 removed outlier: 4.094A pdb=" N HIS u 292 " --> pdb=" O ASN u 288 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA u 293 " --> pdb=" O ALA u 289 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU u 305 " --> pdb=" O HIS u 301 " (cutoff:3.500A) Processing helix chain 'u' and resid 311 through 327 Processing helix chain 'u' and resid 338 through 345 Processing helix chain 'u' and resid 351 through 359 Processing helix chain 'u' and resid 370 through 376 removed outlier: 3.578A pdb=" N MET u 374 " --> pdb=" O LEU u 370 " (cutoff:3.500A) Processing helix chain 'u' and resid 378 through 382 Processing helix chain 'u' and resid 389 through 396 Processing helix chain 'u' and resid 399 through 401 No H-bonds generated for 'chain 'u' and resid 399 through 401' Processing helix chain 'u' and resid 402 through 416 removed outlier: 4.477A pdb=" N VAL u 410 " --> pdb=" O ARG u 406 " (cutoff:3.500A) Processing helix chain 'u' and resid 421 through 427 removed outlier: 3.597A pdb=" N GLN u 426 " --> pdb=" O GLU u 423 " (cutoff:3.500A) Processing helix chain 'u' and resid 428 through 444 Processing helix chain 'u' and resid 451 through 459 removed outlier: 3.673A pdb=" N LEU u 455 " --> pdb=" O GLU u 451 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER u 457 " --> pdb=" O SER u 453 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL u 459 " --> pdb=" O LEU u 455 " (cutoff:3.500A) Processing helix chain 'u' and resid 463 through 476 Processing helix chain 'u' and resid 518 through 523 removed outlier: 3.779A pdb=" N GLN u 522 " --> pdb=" O GLN u 518 " (cutoff:3.500A) Processing helix chain 'u' and resid 525 through 536 removed outlier: 4.030A pdb=" N VAL u 529 " --> pdb=" O ALA u 525 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA u 533 " --> pdb=" O VAL u 529 " (cutoff:3.500A) Processing helix chain 'u' and resid 539 through 560 removed outlier: 3.909A pdb=" N LEU u 543 " --> pdb=" O PRO u 539 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS u 550 " --> pdb=" O LYS u 546 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ALA u 553 " --> pdb=" O GLN u 549 " (cutoff:3.500A) Processing helix chain 'u' and resid 561 through 563 No H-bonds generated for 'chain 'u' and resid 561 through 563' Processing helix chain 'u' and resid 564 through 572 removed outlier: 3.731A pdb=" N ALA u 570 " --> pdb=" O GLN u 566 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG u 572 " --> pdb=" O ILE u 568 " (cutoff:3.500A) Processing helix chain 'v' and resid 37 through 42 removed outlier: 3.747A pdb=" N GLY v 40 " --> pdb=" O LEU v 37 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS v 41 " --> pdb=" O LEU v 38 " (cutoff:3.500A) Processing helix chain 'v' and resid 49 through 55 Processing helix chain 'v' and resid 61 through 66 removed outlier: 3.756A pdb=" N ASP v 65 " --> pdb=" O LEU v 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 70 removed outlier: 3.576A pdb=" N LEU v 70 " --> pdb=" O PRO v 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 67 through 70' Processing helix chain 'v' and resid 76 through 83 Processing helix chain 'v' and resid 96 through 106 removed outlier: 3.907A pdb=" N THR v 101 " --> pdb=" O ASP v 97 " (cutoff:3.500A) Processing helix chain 'v' and resid 107 through 109 No H-bonds generated for 'chain 'v' and resid 107 through 109' Processing helix chain 'v' and resid 128 through 138 removed outlier: 4.337A pdb=" N LYS v 136 " --> pdb=" O TYR v 132 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE v 137 " --> pdb=" O ARG v 133 " (cutoff:3.500A) Processing helix chain 'v' and resid 164 through 177 removed outlier: 4.582A pdb=" N TRP v 170 " --> pdb=" O LEU v 166 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER v 175 " --> pdb=" O GLY v 171 " (cutoff:3.500A) Processing helix chain 'v' and resid 181 through 195 Processing helix chain 'v' and resid 203 through 218 Processing helix chain 'v' and resid 224 through 229 Processing helix chain 'v' and resid 230 through 232 No H-bonds generated for 'chain 'v' and resid 230 through 232' Processing helix chain 'v' and resid 237 through 245 Processing helix chain 'v' and resid 250 through 264 removed outlier: 3.653A pdb=" N ILE v 262 " --> pdb=" O THR v 258 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN v 264 " --> pdb=" O ALA v 260 " (cutoff:3.500A) Processing helix chain 'v' and resid 275 through 280 removed outlier: 4.094A pdb=" N LYS v 279 " --> pdb=" O LYS v 275 " (cutoff:3.500A) Processing helix chain 'v' and resid 304 through 308 removed outlier: 3.602A pdb=" N GLY v 307 " --> pdb=" O ASP v 304 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA v 308 " --> pdb=" O PHE v 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 304 through 308' Processing helix chain 'v' and resid 314 through 321 removed outlier: 4.201A pdb=" N VAL v 318 " --> pdb=" O GLU v 314 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN v 321 " --> pdb=" O SER v 317 " (cutoff:3.500A) Processing helix chain 'v' and resid 329 through 347 removed outlier: 3.526A pdb=" N ILE v 333 " --> pdb=" O LEU v 329 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE v 341 " --> pdb=" O ARG v 337 " (cutoff:3.500A) Processing helix chain 'v' and resid 352 through 357 removed outlier: 3.867A pdb=" N ALA v 357 " --> pdb=" O ILE v 353 " (cutoff:3.500A) Processing helix chain 'v' and resid 363 through 377 removed outlier: 4.074A pdb=" N GLU v 368 " --> pdb=" O PRO v 364 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG v 369 " --> pdb=" O GLU v 365 " (cutoff:3.500A) Processing helix chain 'v' and resid 402 through 420 removed outlier: 3.715A pdb=" N MET v 420 " --> pdb=" O GLN v 416 " (cutoff:3.500A) Processing helix chain 'y' and resid 327 through 338 removed outlier: 4.205A pdb=" N LYS y 331 " --> pdb=" O ALA y 327 " (cutoff:3.500A) Processing helix chain 'y' and resid 346 through 364 removed outlier: 3.777A pdb=" N ILE y 351 " --> pdb=" O ARG y 347 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU y 352 " --> pdb=" O ALA y 348 " (cutoff:3.500A) Processing helix chain 'y' and resid 367 through 384 removed outlier: 4.124A pdb=" N ILE y 371 " --> pdb=" O GLY y 367 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE y 379 " --> pdb=" O LYS y 375 " (cutoff:3.500A) Processing helix chain 'y' and resid 394 through 415 removed outlier: 3.568A pdb=" N ALA y 414 " --> pdb=" O ASP y 410 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN y 415 " --> pdb=" O ILE y 411 " (cutoff:3.500A) Processing helix chain 'y' and resid 443 through 461 removed outlier: 3.574A pdb=" N ASN y 461 " --> pdb=" O LYS y 457 " (cutoff:3.500A) Processing helix chain 'y' and resid 466 through 474 removed outlier: 3.998A pdb=" N VAL y 470 " --> pdb=" O SER y 466 " (cutoff:3.500A) Processing helix chain 'y' and resid 475 through 493 removed outlier: 3.505A pdb=" N VAL y 479 " --> pdb=" O ASP y 475 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU y 491 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU y 492 " --> pdb=" O ARG y 488 " (cutoff:3.500A) Processing helix chain 'y' and resid 495 through 508 removed outlier: 3.592A pdb=" N CYS y 500 " --> pdb=" O THR y 496 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG y 501 " --> pdb=" O GLU y 497 " (cutoff:3.500A) Processing helix chain 'y' and resid 515 through 520 removed outlier: 3.679A pdb=" N ALA y 518 " --> pdb=" O ASP y 515 " (cutoff:3.500A) Processing helix chain 'y' and resid 543 through 558 removed outlier: 3.746A pdb=" N LEU y 547 " --> pdb=" O ASP y 543 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET y 548 " --> pdb=" O SER y 544 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU y 549 " --> pdb=" O ALA y 545 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE y 555 " --> pdb=" O LEU y 551 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA y 557 " --> pdb=" O LYS y 553 " (cutoff:3.500A) Processing helix chain 'y' and resid 563 through 579 removed outlier: 3.758A pdb=" N HIS y 579 " --> pdb=" O HIS y 575 " (cutoff:3.500A) Processing helix chain 'y' and resid 585 through 593 removed outlier: 3.675A pdb=" N SER y 592 " --> pdb=" O LEU y 588 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS y 593 " --> pdb=" O MET y 589 " (cutoff:3.500A) Processing helix chain 'y' and resid 597 through 601 Processing helix chain 'y' and resid 602 through 622 removed outlier: 3.655A pdb=" N ILE y 607 " --> pdb=" O PRO y 603 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU y 608 " --> pdb=" O PRO y 604 " (cutoff:3.500A) Processing helix chain 'y' and resid 626 through 633 removed outlier: 3.633A pdb=" N LEU y 633 " --> pdb=" O ALA y 629 " (cutoff:3.500A) Processing helix chain 'y' and resid 633 through 638 Processing helix chain 'y' and resid 641 through 646 Processing helix chain 'y' and resid 651 through 655 Processing helix chain 'y' and resid 660 through 667 Processing helix chain 'y' and resid 678 through 700 Proline residue: y 696 - end of helix removed outlier: 3.600A pdb=" N ALA y 699 " --> pdb=" O ILE y 695 " (cutoff:3.500A) Processing helix chain 'y' and resid 712 through 723 Processing helix chain 'y' and resid 732 through 743 removed outlier: 3.511A pdb=" N ALA y 743 " --> pdb=" O ALA y 739 " (cutoff:3.500A) Processing helix chain 'y' and resid 749 through 757 Processing helix chain 'y' and resid 758 through 765 removed outlier: 3.698A pdb=" N GLY y 763 " --> pdb=" O GLU y 759 " (cutoff:3.500A) Processing helix chain 'y' and resid 766 through 769 Processing helix chain 'y' and resid 771 through 795 removed outlier: 4.450A pdb=" N VAL y 775 " --> pdb=" O GLU y 771 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG y 776 " --> pdb=" O ALA y 772 " (cutoff:3.500A) Processing helix chain 'y' and resid 814 through 825 removed outlier: 3.683A pdb=" N MET y 825 " --> pdb=" O ILE y 821 " (cutoff:3.500A) Processing helix chain 'y' and resid 851 through 860 Processing helix chain '8' and resid 43 through 54 removed outlier: 3.634A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N HIS 8 52 " --> pdb=" O LYS 8 48 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN 8 54 " --> pdb=" O ILE 8 50 " (cutoff:3.500A) Processing helix chain '8' and resid 97 through 104 removed outlier: 3.904A pdb=" N MET 8 101 " --> pdb=" O VAL 8 97 " (cutoff:3.500A) Processing helix chain '8' and resid 132 through 142 Processing helix chain '8' and resid 173 through 176 No H-bonds generated for 'chain '8' and resid 173 through 176' Processing helix chain '8' and resid 211 through 220 Processing helix chain '8' and resid 232 through 239 Processing helix chain '8' and resid 248 through 278 removed outlier: 3.744A pdb=" N GLN 8 278 " --> pdb=" O LYS 8 274 " (cutoff:3.500A) Processing helix chain '8' and resid 282 through 285 No H-bonds generated for 'chain '8' and resid 282 through 285' Processing helix chain '8' and resid 316 through 350 Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.730A pdb=" N ALA G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 removed outlier: 4.417A pdb=" N LYS G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 66 through 70' Processing helix chain 'G' and resid 77 through 87 removed outlier: 4.474A pdb=" N ARG G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 134 removed outlier: 4.451A pdb=" N VAL G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 182 removed outlier: 4.177A pdb=" N SER G 174 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'K' and resid 56 through 62 Processing helix chain 'K' and resid 65 through 76 Processing helix chain 'M' and resid 99 through 109 removed outlier: 4.492A pdb=" N MET M 105 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.742A pdb=" N LEU L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 147 through 159 removed outlier: 3.966A pdb=" N ILE L 151 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG L 152 " --> pdb=" O ALA L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 162 No H-bonds generated for 'chain 'L' and resid 160 through 162' Processing helix chain 'L' and resid 207 through 215 removed outlier: 3.677A pdb=" N LYS L 212 " --> pdb=" O PRO L 208 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU L 213 " --> pdb=" O VAL L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 245 removed outlier: 3.904A pdb=" N THR L 240 " --> pdb=" O PHE L 236 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 244 " --> pdb=" O THR L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 257 removed outlier: 3.876A pdb=" N LYS L 257 " --> pdb=" O ASP L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.690A pdb=" N PHE L 269 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 275 removed outlier: 3.846A pdb=" N VAL L 274 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 26 removed outlier: 3.944A pdb=" N SER O 26 " --> pdb=" O ASP O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 23 through 26' Processing helix chain 'O' and resid 71 through 76 removed outlier: 3.668A pdb=" N ASN O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 111 Processing helix chain 'O' and resid 159 through 175 removed outlier: 3.754A pdb=" N LYS O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 189 Processing helix chain 'O' and resid 193 through 201 removed outlier: 3.575A pdb=" N LYS O 199 " --> pdb=" O LYS O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 231 Processing helix chain 'N' and resid 11 through 22 removed outlier: 3.768A pdb=" N ALA N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 67 removed outlier: 3.923A pdb=" N LEU N 58 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU N 60 " --> pdb=" O GLU N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 72 No H-bonds generated for 'chain 'N' and resid 70 through 72' Processing helix chain 'N' and resid 85 through 90 Processing helix chain 'N' and resid 90 through 95 Processing helix chain 'N' and resid 130 through 138 Processing helix chain 'N' and resid 168 through 187 removed outlier: 3.883A pdb=" N GLY N 172 " --> pdb=" O ALA N 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET N 174 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 202 removed outlier: 3.587A pdb=" N LEU N 201 " --> pdb=" O MET N 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 49 Processing helix chain 'Q' and resid 50 through 56 removed outlier: 3.818A pdb=" N ALA Q 56 " --> pdb=" O ASP Q 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.601A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 69' Processing helix chain 'P' and resid 70 through 86 removed outlier: 4.280A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN P 83 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 122 removed outlier: 4.406A pdb=" N LEU P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 41 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.543A pdb=" N VAL I 66 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 76 Processing helix chain 'I' and resid 85 through 90 Processing helix chain 'I' and resid 90 through 95 Processing helix chain 'I' and resid 96 through 103 removed outlier: 3.672A pdb=" N GLU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 115 Processing helix chain 'I' and resid 122 through 130 removed outlier: 4.819A pdb=" N TYR I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 150 Processing helix chain '3' and resid 3 through 17 removed outlier: 3.700A pdb=" N ALA 3 9 " --> pdb=" O GLU 3 5 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY 3 17 " --> pdb=" O LYS 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 24 Proline residue: 3 23 - end of helix Processing helix chain '3' and resid 25 through 39 removed outlier: 4.042A pdb=" N LEU 3 29 " --> pdb=" O ASN 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 44 through 57 removed outlier: 3.913A pdb=" N LEU 3 48 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU 3 53 " --> pdb=" O ALA 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 61 Processing helix chain '3' and resid 62 through 75 removed outlier: 3.942A pdb=" N THR 3 66 " --> pdb=" O GLN 3 62 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS 3 72 " --> pdb=" O GLN 3 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR 3 75 " --> pdb=" O LEU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 88 removed outlier: 3.570A pdb=" N LEU 3 84 " --> pdb=" O THR 3 80 " (cutoff:3.500A) Processing helix chain '3' and resid 92 through 95 Processing helix chain '3' and resid 96 through 111 removed outlier: 4.234A pdb=" N LEU 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU 3 109 " --> pdb=" O LEU 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 113 through 121 Processing helix chain '3' and resid 125 through 130 removed outlier: 3.772A pdb=" N GLY 3 130 " --> pdb=" O ASP 3 126 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 150 removed outlier: 3.617A pdb=" N PHE 3 141 " --> pdb=" O SER 3 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY 3 147 " --> pdb=" O CYS 3 143 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE 3 148 " --> pdb=" O HIS 3 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 3 150 " --> pdb=" O VAL 3 146 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 162 Processing helix chain '3' and resid 166 through 178 removed outlier: 3.924A pdb=" N LYS 3 176 " --> pdb=" O VAL 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 196 removed outlier: 3.923A pdb=" N ILE 3 196 " --> pdb=" O GLN 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 216 Processing helix chain '5' and resid 184 through 207 removed outlier: 4.083A pdb=" N CYS 5 202 " --> pdb=" O SER 5 198 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS 5 203 " --> pdb=" O GLN 5 199 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR 5 204 " --> pdb=" O TYR 5 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS 5 207 " --> pdb=" O LYS 5 203 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 218 removed outlier: 3.700A pdb=" N ASN 5 218 " --> pdb=" O PHE 5 214 " (cutoff:3.500A) Processing helix chain '5' and resid 223 through 247 removed outlier: 4.021A pdb=" N VAL 5 227 " --> pdb=" O ASN 5 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL 5 230 " --> pdb=" O SER 5 226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG 5 242 " --> pdb=" O SER 5 238 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN 5 243 " --> pdb=" O ASN 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 252 through 268 removed outlier: 4.145A pdb=" N HIS 5 263 " --> pdb=" O GLU 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 290 removed outlier: 3.677A pdb=" N ARG 5 279 " --> pdb=" O VAL 5 275 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU 5 284 " --> pdb=" O LEU 5 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY 5 285 " --> pdb=" O HIS 5 281 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 303 Processing helix chain '5' and resid 312 through 326 removed outlier: 3.616A pdb=" N VAL 5 319 " --> pdb=" O THR 5 315 " (cutoff:3.500A) Processing helix chain '5' and resid 328 through 335 removed outlier: 3.899A pdb=" N ILE 5 333 " --> pdb=" O TYR 5 329 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG 5 334 " --> pdb=" O GLN 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 335 through 342 removed outlier: 4.341A pdb=" N ILE 5 339 " --> pdb=" O VAL 5 335 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU 5 340 " --> pdb=" O PHE 5 336 " (cutoff:3.500A) Processing helix chain '5' and resid 358 through 375 removed outlier: 4.015A pdb=" N LYS 5 362 " --> pdb=" O GLU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 387 through 401 removed outlier: 3.879A pdb=" N LYS 5 393 " --> pdb=" O GLN 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 405 through 417 removed outlier: 3.758A pdb=" N TYR 5 409 " --> pdb=" O ASP 5 405 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER 5 414 " --> pdb=" O GLU 5 410 " (cutoff:3.500A) Processing helix chain '5' and resid 438 through 462 removed outlier: 3.576A pdb=" N LEU 5 457 " --> pdb=" O GLN 5 453 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE 5 460 " --> pdb=" O GLN 5 456 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG 5 461 " --> pdb=" O LEU 5 457 " (cutoff:3.500A) Processing helix chain '5' and resid 471 through 481 Processing helix chain '5' and resid 491 through 497 Processing helix chain '5' and resid 526 through 549 removed outlier: 3.780A pdb=" N ALA 5 531 " --> pdb=" O MET 5 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 5 545 " --> pdb=" O ASP 5 541 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN 5 546 " --> pdb=" O PHE 5 542 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE 5 547 " --> pdb=" O PHE 5 543 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'u' and resid 490 through 493 removed outlier: 7.257A pdb=" N ASP y 800 " --> pdb=" O VAL u 482 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE u 484 " --> pdb=" O ASP y 800 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE y 802 " --> pdb=" O ILE u 484 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP y 800 " --> pdb=" O VAL y 843 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE y 802 " --> pdb=" O THR y 841 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 51 through 52 removed outlier: 3.983A pdb=" N ILE G 51 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 59 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N VAL G 93 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE G 60 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE G 95 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE G 62 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN G 97 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G 64 " --> pdb=" O GLN G 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.812A pdb=" N ARG G 145 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 32 through 36 Processing sheet with id=AA8, first strand: chain 'H' and resid 64 through 65 Processing sheet with id=AA9, first strand: chain 'K' and resid 35 through 37 Processing sheet with id=AB1, first strand: chain 'M' and resid 96 through 98 Processing sheet with id=AB2, first strand: chain 'L' and resid 105 through 106 removed outlier: 3.616A pdb=" N GLU L 105 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET L 110 " --> pdb=" O LYS L 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 105 through 106 removed outlier: 3.616A pdb=" N GLU L 105 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL L 128 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY L 140 " --> pdb=" O VAL L 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 184 through 188 removed outlier: 3.600A pdb=" N VAL L 184 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS L 222 " --> pdb=" O VAL L 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 45 through 50 removed outlier: 4.134A pdb=" N GLY O 45 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL O 49 " --> pdb=" O ASP O 29 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N CYS O 96 " --> pdb=" O TRP O 30 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP O 32 " --> pdb=" O CYS O 96 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR O 98 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN O 95 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL O 91 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU O 97 " --> pdb=" O GLU O 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 102 through 103 removed outlier: 4.090A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA O 123 " --> pdb=" O CYS O 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 102 through 103 removed outlier: 4.090A pdb=" N VAL O 215 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL O 140 " --> pdb=" O VAL O 210 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL O 210 " --> pdb=" O VAL O 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 38 through 41 removed outlier: 6.815A pdb=" N ILE N 48 " --> pdb=" O TYR N 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 100 removed outlier: 3.999A pdb=" N SER N 75 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL N 123 " --> pdb=" O SER N 75 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU N 122 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N LEU N 147 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL N 124 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR N 144 " --> pdb=" O ILE N 159 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE N 161 " --> pdb=" O THR N 144 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA N 146 " --> pdb=" O ILE N 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 20 through 22 Processing sheet with id=AC2, first strand: chain 'Q' and resid 36 through 43 Processing sheet with id=AC3, first strand: chain 'P' and resid 54 through 57 removed outlier: 3.522A pdb=" N VAL P 56 " --> pdb=" O VAL P 42 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL P 42 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS P 43 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY P 29 " --> pdb=" O HIS P 94 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LYS P 96 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N CYS P 31 " --> pdb=" O LYS P 96 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG P 98 " --> pdb=" O CYS P 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE P 33 " --> pdb=" O ARG P 98 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 180 through 181 removed outlier: 4.126A pdb=" N SER 3 180 " --> pdb=" O PHE 3 188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 469 through 470 removed outlier: 3.593A pdb=" N MET 5 470 " --> pdb=" O PHE 5 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '4' and resid 91 through 94 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '4' and resid 117 through 125 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '4' and resid 128 through 136 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '4' and resid 139 through 142 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '4' and resid 145 through 148 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '4' and resid 168 through 175 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '4' and resid 198 through 202 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '4' and resid 213 through 218 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '4' and resid 231 through 239 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '8' and resid 38 through 41 No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '8' and resid 65 through 71 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '8' and resid 75 through 83 No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain '8' and resid 116 through 121 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '8' and resid 148 through 152 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '8' and resid 164 through 169 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain '8' and resid 198 through 200 No H-bonds generated for sheet with id=AE3 1325 hydrogen bonds defined for protein. 3845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8775 1.33 - 1.46: 6389 1.46 - 1.58: 15777 1.58 - 1.71: 1 1.71 - 1.83: 208 Bond restraints: 31150 Sorted by residual: bond pdb=" C CYS H 64 " pdb=" N GLN H 65 " ideal model delta sigma weight residual 1.332 1.245 0.087 3.60e-02 7.72e+02 5.88e+00 bond pdb=" CB VAL y 358 " pdb=" CG2 VAL y 358 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.80e+00 bond pdb=" CB GLN v 241 " pdb=" CG GLN v 241 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.19e+00 bond pdb=" CB VAL u 34 " pdb=" CG2 VAL u 34 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" C SER v 399 " pdb=" N PRO v 400 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.31e+00 ... (remaining 31145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 40796 2.55 - 5.10: 1310 5.10 - 7.65: 191 7.65 - 10.20: 35 10.20 - 12.75: 6 Bond angle restraints: 42338 Sorted by residual: angle pdb=" N ASN y 423 " pdb=" CA ASN y 423 " pdb=" C ASN y 423 " ideal model delta sigma weight residual 110.42 118.77 -8.35 1.46e+00 4.69e-01 3.27e+01 angle pdb=" C PRO u 333 " pdb=" N GLU u 334 " pdb=" CA GLU u 334 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" N VAL N 7 " pdb=" CA VAL N 7 " pdb=" C VAL N 7 " ideal model delta sigma weight residual 108.80 101.04 7.76 1.46e+00 4.69e-01 2.82e+01 angle pdb=" C ILE 8 211 " pdb=" N ASN 8 212 " pdb=" CA ASN 8 212 " ideal model delta sigma weight residual 120.82 128.69 -7.87 1.50e+00 4.44e-01 2.75e+01 angle pdb=" N PRO y 603 " pdb=" CA PRO y 603 " pdb=" C PRO y 603 " ideal model delta sigma weight residual 110.70 116.81 -6.11 1.22e+00 6.72e-01 2.50e+01 ... (remaining 42333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 18613 35.86 - 71.73: 375 71.73 - 107.59: 18 107.59 - 143.46: 0 143.46 - 179.32: 1 Dihedral angle restraints: 19007 sinusoidal: 6077 harmonic: 12930 Sorted by residual: dihedral pdb=" CD BARG u 14 " pdb=" NE BARG u 14 " pdb=" CZ BARG u 14 " pdb=" NH1BARG u 14 " ideal model delta sinusoidal sigma weight residual 0.00 -179.32 179.32 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA GLY y 421 " pdb=" C GLY y 421 " pdb=" N GLU y 422 " pdb=" CA GLU y 422 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ALA 4 194 " pdb=" C ALA 4 194 " pdb=" N PRO 4 195 " pdb=" CA PRO 4 195 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 19004 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4149 0.078 - 0.156: 802 0.156 - 0.234: 82 0.234 - 0.311: 7 0.311 - 0.389: 3 Chirality restraints: 5043 Sorted by residual: chirality pdb=" CB VAL N 140 " pdb=" CA VAL N 140 " pdb=" CG1 VAL N 140 " pdb=" CG2 VAL N 140 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB VAL P 132 " pdb=" CA VAL P 132 " pdb=" CG1 VAL P 132 " pdb=" CG2 VAL P 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE v 233 " pdb=" CA ILE v 233 " pdb=" CG1 ILE v 233 " pdb=" CG2 ILE v 233 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 5040 not shown) Planarity restraints: 5595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE u 331 " 0.023 2.00e-02 2.50e+03 4.82e-02 2.32e+01 pdb=" C ILE u 331 " -0.083 2.00e-02 2.50e+03 pdb=" O ILE u 331 " 0.032 2.00e-02 2.50e+03 pdb=" N THR u 332 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 4 307 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C PHE 4 307 " -0.072 2.00e-02 2.50e+03 pdb=" O PHE 4 307 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU 4 308 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY 5 258 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C GLY 5 258 " -0.066 2.00e-02 2.50e+03 pdb=" O GLY 5 258 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU 5 259 " 0.022 2.00e-02 2.50e+03 ... (remaining 5592 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7805 2.79 - 3.32: 28667 3.32 - 3.84: 48832 3.84 - 4.37: 52850 4.37 - 4.90: 90666 Nonbonded interactions: 228820 Sorted by model distance: nonbonded pdb=" NE2 GLN v 241 " pdb=" O PHE x 33 " model vdw 2.262 3.120 nonbonded pdb=" O SER y 703 " pdb=" OG SER y 703 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR L 82 " pdb=" O ILE L 162 " model vdw 2.295 3.040 nonbonded pdb=" O HIS y 819 " pdb=" OG SER y 823 " model vdw 2.297 3.040 nonbonded pdb=" O LEU O 62 " pdb=" OG1 THR O 88 " model vdw 2.298 3.040 ... (remaining 228815 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.009 0.087 31150 Z= 0.394 Angle : 1.082 12.746 42338 Z= 0.613 Chirality : 0.061 0.389 5043 Planarity : 0.007 0.088 5595 Dihedral : 15.554 179.320 10553 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.25 % Favored : 90.59 % Rotamer: Outliers : 0.55 % Allowed : 8.43 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.02 (0.11), residues: 4356 helix: -2.29 (0.09), residues: 2106 sheet: -2.55 (0.26), residues: 296 loop : -3.07 (0.12), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 5 TYR 0.034 0.003 TYR x 59 PHE 0.036 0.003 PHE H 47 TRP 0.026 0.003 TRP u 284 HIS 0.015 0.002 HIS y 674 Details of bonding type rmsd covalent geometry : bond 0.00883 (31150) covalent geometry : angle 1.08210 (42338) hydrogen bonds : bond 0.16197 ( 1321) hydrogen bonds : angle 7.49939 ( 3845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 716 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6082 (ttm170) cc_final: 0.5688 (ttm170) REVERT: u 96 MET cc_start: 0.8166 (tpp) cc_final: 0.7254 (tpt) REVERT: u 105 LYS cc_start: 0.7776 (tppt) cc_final: 0.7405 (tppt) REVERT: u 125 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7596 (pt0) REVERT: u 243 MET cc_start: 0.8641 (tpp) cc_final: 0.8419 (tpp) REVERT: u 353 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7873 (ttm170) REVERT: v 281 ILE cc_start: 0.8783 (tp) cc_final: 0.8474 (tp) REVERT: v 313 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7260 (ttp80) REVERT: v 348 HIS cc_start: 0.8457 (m-70) cc_final: 0.8231 (m-70) REVERT: v 368 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7310 (mt-10) REVERT: v 421 ASN cc_start: 0.7457 (m-40) cc_final: 0.7034 (m-40) REVERT: y 459 MET cc_start: 0.8995 (mmp) cc_final: 0.8590 (mmm) REVERT: y 505 LEU cc_start: 0.9046 (tp) cc_final: 0.8753 (tp) REVERT: y 591 MET cc_start: 0.8295 (ttm) cc_final: 0.8073 (ttp) REVERT: y 663 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8165 (mm-30) REVERT: y 691 MET cc_start: 0.8487 (ttp) cc_final: 0.8202 (tmm) REVERT: y 719 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7333 (ttm110) REVERT: y 733 MET cc_start: 0.7489 (ppp) cc_final: 0.7212 (ppp) REVERT: y 735 GLU cc_start: 0.7707 (pm20) cc_final: 0.7487 (pm20) REVERT: y 744 MET cc_start: 0.8756 (ttm) cc_final: 0.8294 (ttm) REVERT: y 758 ASN cc_start: 0.8126 (m110) cc_final: 0.7830 (m110) REVERT: G 73 GLN cc_start: 0.7685 (mt0) cc_final: 0.7407 (mt0) REVERT: G 120 ARG cc_start: 0.5604 (mtt180) cc_final: 0.4865 (mtt-85) REVERT: H 3 LEU cc_start: 0.8185 (mt) cc_final: 0.7861 (mp) REVERT: K 28 ASP cc_start: 0.8795 (t70) cc_final: 0.8559 (t70) REVERT: K 35 ASN cc_start: 0.8693 (m-40) cc_final: 0.8477 (m-40) REVERT: K 61 ARG cc_start: 0.8821 (ttm110) cc_final: 0.7001 (ttt90) REVERT: K 67 ASP cc_start: 0.8892 (t70) cc_final: 0.8649 (t0) REVERT: L 65 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7430 (mmtt) REVERT: L 95 ASP cc_start: 0.8801 (m-30) cc_final: 0.8280 (m-30) REVERT: L 110 MET cc_start: 0.5221 (ptp) cc_final: 0.5004 (ttp) REVERT: L 121 ARG cc_start: 0.6884 (tmm-80) cc_final: 0.5907 (tmm-80) REVERT: L 178 HIS cc_start: 0.6419 (p90) cc_final: 0.5812 (p90) REVERT: L 212 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7869 (mmmt) REVERT: L 215 MET cc_start: 0.7694 (ptp) cc_final: 0.7419 (ptp) REVERT: L 216 MET cc_start: 0.7841 (ttm) cc_final: 0.7388 (mtp) REVERT: L 242 ASP cc_start: 0.8475 (t70) cc_final: 0.8230 (t0) REVERT: L 267 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8188 (tm-30) REVERT: O 28 LYS cc_start: 0.9030 (mttm) cc_final: 0.8782 (mmtm) REVERT: O 76 ASN cc_start: 0.9037 (t0) cc_final: 0.8768 (t0) REVERT: O 117 TRP cc_start: 0.7962 (m-10) cc_final: 0.6641 (m-10) REVERT: N 44 ASP cc_start: 0.7848 (m-30) cc_final: 0.7592 (m-30) REVERT: N 181 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8309 (mm-30) REVERT: N 203 PHE cc_start: 0.7801 (m-10) cc_final: 0.7121 (m-80) REVERT: Q 66 LYS cc_start: 0.9028 (mttt) cc_final: 0.8739 (mttt) REVERT: P 80 ASP cc_start: 0.8863 (m-30) cc_final: 0.8606 (m-30) REVERT: P 117 ARG cc_start: 0.7369 (ttt180) cc_final: 0.7021 (ttm-80) REVERT: P 146 ARG cc_start: 0.3954 (mtt90) cc_final: 0.2675 (ttm170) REVERT: I 70 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7670 (tttt) REVERT: I 124 ARG cc_start: 0.4715 (mtt180) cc_final: 0.2489 (tpt90) REVERT: I 142 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6789 (tm-30) REVERT: x 37 ASP cc_start: 0.7286 (m-30) cc_final: 0.6566 (m-30) REVERT: x 71 TYR cc_start: 0.7896 (t80) cc_final: 0.7515 (t80) outliers start: 14 outliers final: 6 residues processed: 724 average time/residue: 0.2032 time to fit residues: 229.1108 Evaluate side-chains 586 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 580 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 543 LEU Chi-restraints excluded: chain v residue 237 LEU Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 210 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 3.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 345 GLN 6 355 ASN u 44 GLN u 109 GLN u 110 GLN u 175 HIS u 221 ASN u 222 ASN u 229 HIS u 236 GLN u 392 ASN u 466 GLN u 522 GLN v 231 ASN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 252 HIS v 282 GLN v 377 ASN y 364 ASN ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 432 HIS y 460 GLN y 852 GLN G 25 GLN G 33 ASN G 68 GLN G 165 ASN G 186 ASN H 51 GLN M 93 GLN L 136 HIS L 272 HIS O 186 ASN O 208 HIS N 24 HIS N 29 ASN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 ASN ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 GLN ** N 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN P 94 HIS I 36 GLN I 101 HIS I 105 ASN I 123 HIS x 31 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.165950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129282 restraints weight = 66053.731| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.52 r_work: 0.3543 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 31150 Z= 0.277 Angle : 0.747 11.691 42338 Z= 0.403 Chirality : 0.046 0.167 5043 Planarity : 0.005 0.067 5595 Dihedral : 7.237 176.951 4693 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 3.09 % Allowed : 17.93 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.18 (0.12), residues: 4356 helix: -1.42 (0.10), residues: 2140 sheet: -2.38 (0.29), residues: 268 loop : -2.85 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG y 441 TYR 0.023 0.002 TYR u 54 PHE 0.028 0.002 PHE H 47 TRP 0.026 0.002 TRP u 284 HIS 0.013 0.001 HIS L 272 Details of bonding type rmsd covalent geometry : bond 0.00614 (31150) covalent geometry : angle 0.74695 (42338) hydrogen bonds : bond 0.04920 ( 1321) hydrogen bonds : angle 5.83337 ( 3845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 616 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6440 (ttm170) cc_final: 0.5824 (ttm170) REVERT: u 96 MET cc_start: 0.8507 (tpp) cc_final: 0.7765 (tpt) REVERT: u 105 LYS cc_start: 0.7859 (tppt) cc_final: 0.7507 (tppt) REVERT: u 125 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7939 (pt0) REVERT: u 243 MET cc_start: 0.8918 (tpp) cc_final: 0.8716 (tpp) REVERT: u 353 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7964 (ttm110) REVERT: u 382 TYR cc_start: 0.7243 (m-10) cc_final: 0.6515 (m-10) REVERT: v 313 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7267 (ttp80) REVERT: v 348 HIS cc_start: 0.8685 (m-70) cc_final: 0.8450 (m-70) REVERT: v 368 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7370 (mt-10) REVERT: v 401 TYR cc_start: 0.5677 (t80) cc_final: 0.5315 (m-80) REVERT: y 459 MET cc_start: 0.9000 (mmp) cc_final: 0.8338 (mmm) REVERT: y 505 LEU cc_start: 0.9097 (tp) cc_final: 0.8856 (tp) REVERT: y 709 MET cc_start: 0.7917 (ptt) cc_final: 0.7600 (ptt) REVERT: y 733 MET cc_start: 0.8221 (ppp) cc_final: 0.7780 (ppp) REVERT: y 735 GLU cc_start: 0.7986 (pm20) cc_final: 0.7691 (pm20) REVERT: y 744 MET cc_start: 0.8888 (ttm) cc_final: 0.8479 (ttm) REVERT: y 825 MET cc_start: 0.7277 (mpp) cc_final: 0.7075 (ptp) REVERT: y 846 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7989 (mmm-85) REVERT: y 859 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7712 (mm) REVERT: G 73 GLN cc_start: 0.8050 (mt0) cc_final: 0.7430 (pt0) REVERT: G 160 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7811 (ttmt) REVERT: G 165 ASN cc_start: 0.8569 (t0) cc_final: 0.8341 (t0) REVERT: H 3 LEU cc_start: 0.8096 (mt) cc_final: 0.7861 (mp) REVERT: K 28 ASP cc_start: 0.9020 (t70) cc_final: 0.8816 (t70) REVERT: K 35 ASN cc_start: 0.8729 (m-40) cc_final: 0.8443 (m-40) REVERT: K 61 ARG cc_start: 0.8942 (ttm110) cc_final: 0.7142 (ttt90) REVERT: L 68 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6479 (mtp180) REVERT: L 95 ASP cc_start: 0.8579 (m-30) cc_final: 0.7861 (m-30) REVERT: L 121 ARG cc_start: 0.6502 (tmm-80) cc_final: 0.5516 (tmm-80) REVERT: L 178 HIS cc_start: 0.6316 (p90) cc_final: 0.6076 (p-80) REVERT: L 216 MET cc_start: 0.7906 (ttm) cc_final: 0.7571 (mtp) REVERT: L 267 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8093 (tm-30) REVERT: O 63 LYS cc_start: 0.8282 (mttp) cc_final: 0.7985 (mtmm) REVERT: O 155 TYR cc_start: 0.8990 (m-80) cc_final: 0.8445 (m-80) REVERT: N 165 ASN cc_start: 0.8691 (p0) cc_final: 0.8378 (p0) REVERT: N 181 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8520 (mm-30) REVERT: N 203 PHE cc_start: 0.7825 (m-10) cc_final: 0.7165 (m-80) REVERT: Q 66 LYS cc_start: 0.8967 (mttt) cc_final: 0.8669 (mttt) REVERT: P 76 LEU cc_start: 0.8238 (mt) cc_final: 0.7744 (tt) REVERT: P 80 ASP cc_start: 0.8983 (m-30) cc_final: 0.8533 (m-30) REVERT: P 90 ILE cc_start: 0.9068 (mm) cc_final: 0.8819 (mm) REVERT: P 146 ARG cc_start: 0.4474 (mtt90) cc_final: 0.2591 (ttm170) REVERT: I 70 LYS cc_start: 0.8478 (mtmt) cc_final: 0.7682 (tttm) REVERT: I 124 ARG cc_start: 0.5008 (mtt180) cc_final: 0.2614 (tmt170) REVERT: I 142 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6811 (tm-30) REVERT: x 71 TYR cc_start: 0.8204 (t80) cc_final: 0.7654 (t80) REVERT: x 77 GLU cc_start: 0.7486 (pm20) cc_final: 0.7146 (pm20) outliers start: 78 outliers final: 52 residues processed: 655 average time/residue: 0.1972 time to fit residues: 205.4981 Evaluate side-chains 619 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 565 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 262 LEU Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 357 THR Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 802 ILE Chi-restraints excluded: chain y residue 846 ARG Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 272 HIS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain x residue 35 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 239 optimal weight: 0.0070 chunk 142 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 377 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 413 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 chunk 42 optimal weight: 50.0000 chunk 376 optimal weight: 8.9990 overall best weight: 2.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 345 GLN u 109 GLN u 200 ASN u 236 GLN v 231 ASN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 120 GLN L 272 HIS ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN x 57 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.168388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130016 restraints weight = 84662.990| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.89 r_work: 0.3577 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31150 Z= 0.161 Angle : 0.621 10.196 42338 Z= 0.333 Chirality : 0.043 0.254 5043 Planarity : 0.004 0.063 5595 Dihedral : 6.543 175.980 4687 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.05 % Allowed : 21.25 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.12), residues: 4356 helix: -0.82 (0.11), residues: 2124 sheet: -2.19 (0.30), residues: 258 loop : -2.58 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 438 TYR 0.039 0.002 TYR I 38 PHE 0.026 0.001 PHE G 135 TRP 0.021 0.001 TRP u 284 HIS 0.005 0.001 HIS u 301 Details of bonding type rmsd covalent geometry : bond 0.00350 (31150) covalent geometry : angle 0.62138 (42338) hydrogen bonds : bond 0.03960 ( 1321) hydrogen bonds : angle 5.20963 ( 3845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 645 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6595 (ttm170) cc_final: 0.5945 (ttm170) REVERT: u 19 LEU cc_start: 0.8991 (mt) cc_final: 0.8732 (mp) REVERT: u 96 MET cc_start: 0.8527 (tpp) cc_final: 0.7818 (tpt) REVERT: u 105 LYS cc_start: 0.7786 (tppt) cc_final: 0.7510 (tppt) REVERT: u 243 MET cc_start: 0.8907 (tpp) cc_final: 0.8655 (tpp) REVERT: u 382 TYR cc_start: 0.7237 (m-10) cc_final: 0.6793 (m-10) REVERT: v 249 MET cc_start: 0.6752 (mtt) cc_final: 0.6443 (mtt) REVERT: v 368 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7149 (mt-10) REVERT: v 420 MET cc_start: 0.5779 (mtm) cc_final: 0.5425 (mtm) REVERT: v 421 ASN cc_start: 0.7882 (m-40) cc_final: 0.7551 (m-40) REVERT: y 459 MET cc_start: 0.8861 (mmp) cc_final: 0.8266 (mmm) REVERT: y 490 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (mp) REVERT: y 505 LEU cc_start: 0.9092 (tp) cc_final: 0.8862 (tp) REVERT: y 707 ARG cc_start: 0.6576 (mmt180) cc_final: 0.6230 (mmt180) REVERT: y 709 MET cc_start: 0.7918 (ptt) cc_final: 0.7509 (ptt) REVERT: y 733 MET cc_start: 0.8137 (ppp) cc_final: 0.7668 (ppp) REVERT: y 758 ASN cc_start: 0.8550 (m-40) cc_final: 0.8239 (m110) REVERT: y 810 MET cc_start: 0.8457 (ttm) cc_final: 0.8114 (mtp) REVERT: y 846 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8311 (mmm-85) REVERT: y 848 GLU cc_start: 0.7822 (pt0) cc_final: 0.7559 (pt0) REVERT: y 859 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7679 (mm) REVERT: G 69 LEU cc_start: 0.9068 (tp) cc_final: 0.8702 (tp) REVERT: H 3 LEU cc_start: 0.7957 (mt) cc_final: 0.7696 (mp) REVERT: K 35 ASN cc_start: 0.8705 (m-40) cc_final: 0.8357 (m-40) REVERT: K 61 ARG cc_start: 0.8793 (ttm110) cc_final: 0.6936 (ttt90) REVERT: K 67 ASP cc_start: 0.8938 (t0) cc_final: 0.8691 (t0) REVERT: L 68 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6596 (mtp180) REVERT: L 94 ILE cc_start: 0.8336 (mm) cc_final: 0.8121 (mm) REVERT: L 95 ASP cc_start: 0.8573 (m-30) cc_final: 0.8036 (m-30) REVERT: L 178 HIS cc_start: 0.6366 (p90) cc_final: 0.6075 (p-80) REVERT: L 212 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7542 (mmmt) REVERT: L 215 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7249 (ptm) REVERT: L 216 MET cc_start: 0.8043 (ttm) cc_final: 0.7495 (mtp) REVERT: L 256 TRP cc_start: 0.8828 (m-10) cc_final: 0.6937 (m100) REVERT: L 267 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8194 (tm-30) REVERT: O 85 LYS cc_start: 0.7783 (ptpt) cc_final: 0.7408 (mttp) REVERT: O 110 MET cc_start: 0.8798 (tpp) cc_final: 0.8192 (ttm) REVERT: O 155 TYR cc_start: 0.8921 (m-10) cc_final: 0.8414 (m-80) REVERT: O 209 ASP cc_start: 0.8918 (m-30) cc_final: 0.8506 (m-30) REVERT: N 29 ASN cc_start: 0.8677 (m-40) cc_final: 0.7922 (m-40) REVERT: N 165 ASN cc_start: 0.8662 (p0) cc_final: 0.8291 (p0) REVERT: N 203 PHE cc_start: 0.7781 (m-10) cc_final: 0.7168 (m-80) REVERT: Q 66 LYS cc_start: 0.9044 (mttt) cc_final: 0.8784 (mttt) REVERT: P 76 LEU cc_start: 0.8304 (mt) cc_final: 0.7702 (tt) REVERT: P 80 ASP cc_start: 0.8953 (m-30) cc_final: 0.8448 (m-30) REVERT: P 113 GLN cc_start: 0.7448 (pp30) cc_final: 0.7178 (pp30) REVERT: P 146 ARG cc_start: 0.4524 (mtt90) cc_final: 0.2765 (ttm170) REVERT: I 70 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7732 (tttm) REVERT: I 124 ARG cc_start: 0.5150 (mtt180) cc_final: 0.2949 (tmt170) REVERT: I 142 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6933 (tm-30) REVERT: x 23 GLU cc_start: 0.5707 (mp0) cc_final: 0.5393 (mp0) REVERT: x 37 ASP cc_start: 0.7716 (m-30) cc_final: 0.7455 (m-30) REVERT: x 71 TYR cc_start: 0.8162 (t80) cc_final: 0.7559 (t80) outliers start: 77 outliers final: 56 residues processed: 687 average time/residue: 0.2033 time to fit residues: 221.7497 Evaluate side-chains 643 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 584 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 301 HIS Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 490 LEU Chi-restraints excluded: chain y residue 496 THR Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 738 VAL Chi-restraints excluded: chain y residue 802 ILE Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 14 ASP Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 271 optimal weight: 4.9990 chunk 375 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 0.0970 chunk 208 optimal weight: 50.0000 chunk 280 optimal weight: 0.1980 chunk 301 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 391 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 109 GLN v 231 ASN v 244 ASN v 416 GLN ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 76 GLN G 165 ASN Q 86 ASN x 57 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.134198 restraints weight = 69088.678| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.73 r_work: 0.3611 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31150 Z= 0.113 Angle : 0.574 9.059 42338 Z= 0.304 Chirality : 0.042 0.230 5043 Planarity : 0.004 0.064 5595 Dihedral : 6.100 178.452 4687 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.56 % Allowed : 22.24 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 4356 helix: -0.46 (0.11), residues: 2125 sheet: -1.96 (0.30), residues: 263 loop : -2.39 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 81 TYR 0.049 0.001 TYR I 38 PHE 0.016 0.001 PHE G 135 TRP 0.018 0.001 TRP u 284 HIS 0.010 0.001 HIS L 272 Details of bonding type rmsd covalent geometry : bond 0.00247 (31150) covalent geometry : angle 0.57369 (42338) hydrogen bonds : bond 0.03467 ( 1321) hydrogen bonds : angle 4.84392 ( 3845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 642 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6637 (ttm170) cc_final: 0.5860 (ttm170) REVERT: u 96 MET cc_start: 0.8475 (tpp) cc_final: 0.7588 (tpt) REVERT: u 105 LYS cc_start: 0.7691 (tppt) cc_final: 0.7360 (tppt) REVERT: u 243 MET cc_start: 0.8871 (tpp) cc_final: 0.8581 (tpp) REVERT: u 318 MET cc_start: 0.6830 (ttt) cc_final: 0.6532 (ttm) REVERT: u 382 TYR cc_start: 0.7058 (m-10) cc_final: 0.6806 (m-10) REVERT: u 526 MET cc_start: 0.8002 (ppp) cc_final: 0.7798 (ppp) REVERT: v 326 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6718 (p) REVERT: v 368 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7233 (mt-10) REVERT: v 401 TYR cc_start: 0.5658 (t80) cc_final: 0.4903 (m-80) REVERT: v 421 ASN cc_start: 0.7927 (m-40) cc_final: 0.7630 (m-40) REVERT: y 505 LEU cc_start: 0.9044 (tp) cc_final: 0.8831 (tp) REVERT: y 707 ARG cc_start: 0.6823 (mmt180) cc_final: 0.6576 (mmt180) REVERT: y 709 MET cc_start: 0.7829 (ptt) cc_final: 0.7420 (ptt) REVERT: y 733 MET cc_start: 0.8068 (ppp) cc_final: 0.7813 (ppp) REVERT: y 735 GLU cc_start: 0.8101 (pm20) cc_final: 0.7736 (pm20) REVERT: y 758 ASN cc_start: 0.8526 (m-40) cc_final: 0.8127 (m110) REVERT: y 824 LYS cc_start: 0.8940 (tptp) cc_final: 0.8591 (ttmt) REVERT: y 846 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8219 (mmm-85) REVERT: y 848 GLU cc_start: 0.7892 (pt0) cc_final: 0.7280 (pt0) REVERT: y 859 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7720 (mm) REVERT: G 69 LEU cc_start: 0.8955 (tp) cc_final: 0.8575 (tp) REVERT: H 3 LEU cc_start: 0.7926 (mt) cc_final: 0.7725 (mp) REVERT: K 2 GLN cc_start: 0.9247 (mt0) cc_final: 0.8713 (mp10) REVERT: K 35 ASN cc_start: 0.8713 (m-40) cc_final: 0.8482 (m-40) REVERT: K 61 ARG cc_start: 0.8783 (ttm110) cc_final: 0.7018 (ttt90) REVERT: K 67 ASP cc_start: 0.8912 (t0) cc_final: 0.8565 (t0) REVERT: L 68 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6582 (mtp180) REVERT: L 72 ASP cc_start: 0.8486 (m-30) cc_final: 0.7466 (p0) REVERT: L 94 ILE cc_start: 0.8184 (mm) cc_final: 0.7923 (mm) REVERT: L 95 ASP cc_start: 0.8477 (m-30) cc_final: 0.7774 (m-30) REVERT: L 178 HIS cc_start: 0.6411 (p90) cc_final: 0.6180 (p-80) REVERT: L 212 LYS cc_start: 0.7861 (mmmt) cc_final: 0.7645 (mmmt) REVERT: L 216 MET cc_start: 0.8007 (ttm) cc_final: 0.7493 (mtp) REVERT: L 256 TRP cc_start: 0.8799 (m-10) cc_final: 0.7059 (m100) REVERT: O 46 LYS cc_start: 0.8458 (mptt) cc_final: 0.8198 (mptt) REVERT: O 85 LYS cc_start: 0.7730 (ptpt) cc_final: 0.7447 (mttp) REVERT: O 110 MET cc_start: 0.8724 (tpp) cc_final: 0.8173 (ttm) REVERT: O 155 TYR cc_start: 0.8712 (m-10) cc_final: 0.8276 (m-80) REVERT: O 209 ASP cc_start: 0.8867 (m-30) cc_final: 0.8540 (m-30) REVERT: N 111 GLN cc_start: 0.8196 (pp30) cc_final: 0.7995 (pp30) REVERT: N 165 ASN cc_start: 0.8550 (p0) cc_final: 0.8119 (p0) REVERT: N 203 PHE cc_start: 0.7655 (m-10) cc_final: 0.7078 (m-80) REVERT: P 76 LEU cc_start: 0.8299 (mt) cc_final: 0.7729 (tt) REVERT: P 80 ASP cc_start: 0.8854 (m-30) cc_final: 0.8272 (m-30) REVERT: P 146 ARG cc_start: 0.4447 (mtt90) cc_final: 0.2763 (ttm170) REVERT: I 70 LYS cc_start: 0.8459 (mtmt) cc_final: 0.7684 (tttm) REVERT: I 124 ARG cc_start: 0.4911 (mtt180) cc_final: 0.3080 (tmt170) REVERT: I 142 GLU cc_start: 0.7450 (tm-30) cc_final: 0.6937 (tm-30) REVERT: x 44 ASP cc_start: 0.7560 (t0) cc_final: 0.7356 (t70) REVERT: x 71 TYR cc_start: 0.8087 (t80) cc_final: 0.7503 (t80) outliers start: 90 outliers final: 58 residues processed: 692 average time/residue: 0.1858 time to fit residues: 205.1860 Evaluate side-chains 645 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 585 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 666 GLU Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 738 VAL Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 271 ASP Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain x residue 35 LYS Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 284 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 431 optimal weight: 0.0770 chunk 161 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 258 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 211 optimal weight: 50.0000 chunk 2 optimal weight: 8.9990 chunk 160 optimal weight: 0.2980 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 109 GLN u 211 HIS v 231 ASN ** v 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN H 49 HIS x 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132914 restraints weight = 73126.135| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.71 r_work: 0.3605 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31150 Z= 0.129 Angle : 0.585 9.852 42338 Z= 0.308 Chirality : 0.042 0.208 5043 Planarity : 0.004 0.099 5595 Dihedral : 5.965 179.126 4687 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.76 % Allowed : 23.23 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 4356 helix: -0.27 (0.11), residues: 2134 sheet: -1.80 (0.30), residues: 261 loop : -2.38 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG x 26 TYR 0.044 0.001 TYR I 38 PHE 0.023 0.001 PHE N 116 TRP 0.018 0.001 TRP u 284 HIS 0.004 0.001 HIS y 674 Details of bonding type rmsd covalent geometry : bond 0.00288 (31150) covalent geometry : angle 0.58461 (42338) hydrogen bonds : bond 0.03407 ( 1321) hydrogen bonds : angle 4.71927 ( 3845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 605 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 320 MET cc_start: 0.6543 (tpp) cc_final: 0.6149 (tpp) REVERT: 6 330 ARG cc_start: 0.6640 (ttm170) cc_final: 0.5792 (ttm170) REVERT: 6 346 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7316 (mp10) REVERT: u 33 ASP cc_start: 0.8726 (m-30) cc_final: 0.8458 (t0) REVERT: u 96 MET cc_start: 0.8438 (tpp) cc_final: 0.7732 (tpt) REVERT: u 105 LYS cc_start: 0.7741 (tppt) cc_final: 0.7453 (tppt) REVERT: u 243 MET cc_start: 0.8877 (tpp) cc_final: 0.8590 (tpp) REVERT: u 318 MET cc_start: 0.6986 (ttt) cc_final: 0.6560 (ttm) REVERT: u 382 TYR cc_start: 0.7157 (m-10) cc_final: 0.6812 (m-10) REVERT: u 434 ASN cc_start: 0.8197 (t0) cc_final: 0.7800 (t0) REVERT: v 249 MET cc_start: 0.5625 (mtt) cc_final: 0.5283 (mtt) REVERT: v 368 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7296 (mt-10) REVERT: v 401 TYR cc_start: 0.5857 (t80) cc_final: 0.5402 (m-80) REVERT: y 459 MET cc_start: 0.8648 (mmm) cc_final: 0.7970 (mmm) REVERT: y 495 THR cc_start: 0.7906 (OUTLIER) cc_final: 0.7569 (p) REVERT: y 707 ARG cc_start: 0.6952 (mmt180) cc_final: 0.6718 (mmt180) REVERT: y 709 MET cc_start: 0.7914 (ptt) cc_final: 0.7485 (ptt) REVERT: y 733 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7900 (ppp) REVERT: y 735 GLU cc_start: 0.8128 (pm20) cc_final: 0.7731 (pm20) REVERT: y 758 ASN cc_start: 0.8518 (m-40) cc_final: 0.8115 (m110) REVERT: y 810 MET cc_start: 0.8371 (ttm) cc_final: 0.8077 (mtp) REVERT: y 824 LYS cc_start: 0.8833 (tptp) cc_final: 0.8455 (ttmt) REVERT: y 846 ARG cc_start: 0.8561 (mmm160) cc_final: 0.8298 (mmm-85) REVERT: y 848 GLU cc_start: 0.7954 (pt0) cc_final: 0.7395 (pt0) REVERT: y 859 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7773 (mm) REVERT: K 2 GLN cc_start: 0.9128 (mt0) cc_final: 0.8621 (mp10) REVERT: K 35 ASN cc_start: 0.8641 (m-40) cc_final: 0.8340 (m-40) REVERT: K 61 ARG cc_start: 0.8777 (ttm110) cc_final: 0.7037 (ttt90) REVERT: K 67 ASP cc_start: 0.8941 (t0) cc_final: 0.8662 (t0) REVERT: L 68 ARG cc_start: 0.6774 (mtt180) cc_final: 0.6541 (mtp180) REVERT: L 72 ASP cc_start: 0.8453 (m-30) cc_final: 0.7461 (p0) REVERT: L 95 ASP cc_start: 0.8470 (m-30) cc_final: 0.7795 (m-30) REVERT: L 178 HIS cc_start: 0.6401 (p90) cc_final: 0.6157 (p-80) REVERT: L 212 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7603 (mmmt) REVERT: L 216 MET cc_start: 0.8004 (ttm) cc_final: 0.7582 (mtp) REVERT: L 256 TRP cc_start: 0.8779 (m-10) cc_final: 0.7066 (m100) REVERT: O 46 LYS cc_start: 0.8455 (mptt) cc_final: 0.8173 (mptt) REVERT: O 76 ASN cc_start: 0.9130 (t0) cc_final: 0.8734 (t0) REVERT: O 110 MET cc_start: 0.8717 (tpp) cc_final: 0.8188 (ttm) REVERT: O 155 TYR cc_start: 0.8683 (m-10) cc_final: 0.8234 (m-80) REVERT: O 209 ASP cc_start: 0.8826 (m-30) cc_final: 0.8491 (m-30) REVERT: N 165 ASN cc_start: 0.8523 (p0) cc_final: 0.8043 (p0) REVERT: P 76 LEU cc_start: 0.8208 (mt) cc_final: 0.7599 (tt) REVERT: P 80 ASP cc_start: 0.8853 (m-30) cc_final: 0.8295 (m-30) REVERT: P 146 ARG cc_start: 0.4533 (mtt90) cc_final: 0.2882 (ttm170) REVERT: I 70 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7700 (tttm) REVERT: I 103 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7723 (mm-30) REVERT: I 124 ARG cc_start: 0.5194 (mtt180) cc_final: 0.3333 (tmt170) REVERT: I 142 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7218 (tm-30) REVERT: x 44 ASP cc_start: 0.7536 (t0) cc_final: 0.7332 (t70) REVERT: x 71 TYR cc_start: 0.8088 (t80) cc_final: 0.7499 (t80) outliers start: 95 outliers final: 69 residues processed: 663 average time/residue: 0.1872 time to fit residues: 198.3122 Evaluate side-chains 651 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 578 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain 6 residue 346 GLN Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 301 HIS Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 666 GLU Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 733 MET Chi-restraints excluded: chain y residue 798 VAL Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 323 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 422 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 294 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 409 optimal weight: 8.9990 chunk 230 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 353 optimal weight: 0.8980 chunk 213 optimal weight: 40.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 109 GLN ** v 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 416 GLN ** y 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 852 GLN G 126 HIS N 169 HIS x 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.169798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.130726 restraints weight = 74691.270| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.48 r_work: 0.3594 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31150 Z= 0.167 Angle : 0.606 9.497 42338 Z= 0.317 Chirality : 0.043 0.274 5043 Planarity : 0.004 0.063 5595 Dihedral : 5.989 179.221 4687 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.19 % Allowed : 23.51 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 4356 helix: -0.20 (0.11), residues: 2136 sheet: -1.94 (0.29), residues: 279 loop : -2.35 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG x 26 TYR 0.039 0.001 TYR I 38 PHE 0.020 0.001 PHE H 47 TRP 0.018 0.001 TRP u 284 HIS 0.006 0.001 HIS G 126 Details of bonding type rmsd covalent geometry : bond 0.00378 (31150) covalent geometry : angle 0.60605 (42338) hydrogen bonds : bond 0.03457 ( 1321) hydrogen bonds : angle 4.72514 ( 3845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 595 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 320 MET cc_start: 0.6627 (tpp) cc_final: 0.6124 (tpp) REVERT: 6 330 ARG cc_start: 0.6671 (ttm170) cc_final: 0.5769 (ttm170) REVERT: u 96 MET cc_start: 0.8455 (tpp) cc_final: 0.7862 (tpt) REVERT: u 105 LYS cc_start: 0.7856 (tppt) cc_final: 0.7589 (tppt) REVERT: u 243 MET cc_start: 0.8838 (tpp) cc_final: 0.8565 (tpp) REVERT: u 318 MET cc_start: 0.7064 (ttt) cc_final: 0.6785 (ttm) REVERT: u 382 TYR cc_start: 0.7166 (m-10) cc_final: 0.6692 (m-10) REVERT: u 434 ASN cc_start: 0.8258 (t0) cc_final: 0.7875 (t0) REVERT: v 249 MET cc_start: 0.5861 (mtt) cc_final: 0.5519 (mtt) REVERT: v 368 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7349 (mt-10) REVERT: v 401 TYR cc_start: 0.5856 (t80) cc_final: 0.5339 (m-80) REVERT: y 459 MET cc_start: 0.8730 (mmm) cc_final: 0.8191 (mmm) REVERT: y 495 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7508 (p) REVERT: y 648 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8093 (mm-40) REVERT: y 707 ARG cc_start: 0.7030 (mmt180) cc_final: 0.6795 (mmt180) REVERT: y 709 MET cc_start: 0.7894 (ptt) cc_final: 0.7484 (ptt) REVERT: y 733 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (ppp) REVERT: y 758 ASN cc_start: 0.8506 (m-40) cc_final: 0.8291 (m-40) REVERT: y 810 MET cc_start: 0.8393 (ttm) cc_final: 0.8170 (mtp) REVERT: y 824 LYS cc_start: 0.8857 (tptp) cc_final: 0.8436 (ttmt) REVERT: y 846 ARG cc_start: 0.8518 (mmm160) cc_final: 0.8060 (mmm-85) REVERT: y 848 GLU cc_start: 0.7968 (pt0) cc_final: 0.7392 (pt0) REVERT: y 859 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7743 (mm) REVERT: K 35 ASN cc_start: 0.8644 (m-40) cc_final: 0.8336 (m-40) REVERT: K 61 ARG cc_start: 0.8768 (ttm110) cc_final: 0.7038 (ttt90) REVERT: K 67 ASP cc_start: 0.8981 (t0) cc_final: 0.8706 (t0) REVERT: L 68 ARG cc_start: 0.6753 (mtt180) cc_final: 0.6514 (mtp180) REVERT: L 72 ASP cc_start: 0.8410 (m-30) cc_final: 0.7468 (p0) REVERT: L 95 ASP cc_start: 0.8438 (m-30) cc_final: 0.7752 (m-30) REVERT: L 178 HIS cc_start: 0.6365 (p90) cc_final: 0.5859 (p90) REVERT: L 216 MET cc_start: 0.8020 (ttm) cc_final: 0.7506 (mtp) REVERT: L 223 TYR cc_start: 0.7599 (m-10) cc_final: 0.7250 (m-10) REVERT: L 256 TRP cc_start: 0.8796 (m-10) cc_final: 0.7045 (m100) REVERT: O 46 LYS cc_start: 0.8489 (mptt) cc_final: 0.8217 (mptt) REVERT: O 155 TYR cc_start: 0.8700 (m-10) cc_final: 0.8269 (m-80) REVERT: O 209 ASP cc_start: 0.8806 (m-30) cc_final: 0.8475 (m-30) REVERT: N 165 ASN cc_start: 0.8541 (p0) cc_final: 0.8093 (p0) REVERT: Q 95 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5793 (mmt180) REVERT: P 76 LEU cc_start: 0.8237 (mt) cc_final: 0.7610 (tt) REVERT: P 80 ASP cc_start: 0.8902 (m-30) cc_final: 0.8366 (m-30) REVERT: P 146 ARG cc_start: 0.4579 (mtt90) cc_final: 0.2916 (ttm170) REVERT: I 70 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7696 (tttm) REVERT: I 124 ARG cc_start: 0.5381 (mtt180) cc_final: 0.3359 (tmt170) REVERT: I 142 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7192 (tm-30) REVERT: x 44 ASP cc_start: 0.7584 (t0) cc_final: 0.7362 (t70) REVERT: x 71 TYR cc_start: 0.8095 (t80) cc_final: 0.7512 (t80) outliers start: 106 outliers final: 85 residues processed: 655 average time/residue: 0.1852 time to fit residues: 195.1701 Evaluate side-chains 658 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 569 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 69 GLU Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 259 LEU Chi-restraints excluded: chain u residue 301 HIS Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 496 THR Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 546 VAL Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 733 MET Chi-restraints excluded: chain y residue 779 LEU Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 335 optimal weight: 0.5980 chunk 214 optimal weight: 40.0000 chunk 286 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 364 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 312 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 297 HIS v 231 ASN ** v 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 758 ASN y 852 GLN x 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.169043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130281 restraints weight = 70213.243| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.35 r_work: 0.3590 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31150 Z= 0.184 Angle : 0.620 9.155 42338 Z= 0.324 Chirality : 0.044 0.333 5043 Planarity : 0.004 0.062 5595 Dihedral : 6.031 179.848 4687 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.38 % Favored : 91.60 % Rotamer: Outliers : 4.83 % Allowed : 23.35 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.13), residues: 4356 helix: -0.14 (0.11), residues: 2142 sheet: -2.00 (0.29), residues: 279 loop : -2.33 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 26 TYR 0.030 0.001 TYR N 156 PHE 0.021 0.001 PHE H 47 TRP 0.033 0.002 TRP 6 347 HIS 0.007 0.001 HIS G 126 Details of bonding type rmsd covalent geometry : bond 0.00417 (31150) covalent geometry : angle 0.61984 (42338) hydrogen bonds : bond 0.03507 ( 1321) hydrogen bonds : angle 4.72667 ( 3845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 577 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6711 (ttm170) cc_final: 0.5744 (ttm170) REVERT: 6 345 GLN cc_start: 0.6477 (tm-30) cc_final: 0.5526 (mt0) REVERT: u 96 MET cc_start: 0.8460 (tpp) cc_final: 0.7927 (tpt) REVERT: u 105 LYS cc_start: 0.7899 (tppt) cc_final: 0.7616 (tppt) REVERT: u 243 MET cc_start: 0.8848 (tpp) cc_final: 0.8587 (tpp) REVERT: u 328 SER cc_start: 0.9099 (m) cc_final: 0.8884 (m) REVERT: u 382 TYR cc_start: 0.7246 (m-10) cc_final: 0.6968 (m-10) REVERT: u 434 ASN cc_start: 0.8225 (t0) cc_final: 0.7885 (t0) REVERT: v 249 MET cc_start: 0.6274 (mtt) cc_final: 0.5935 (mtt) REVERT: v 368 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7248 (mt-10) REVERT: v 401 TYR cc_start: 0.5810 (t80) cc_final: 0.5332 (m-80) REVERT: y 459 MET cc_start: 0.8783 (mmm) cc_final: 0.8535 (mmm) REVERT: y 495 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7838 (m) REVERT: y 648 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8211 (mm-40) REVERT: y 707 ARG cc_start: 0.6960 (mmt180) cc_final: 0.6722 (mmt180) REVERT: y 709 MET cc_start: 0.8014 (ptt) cc_final: 0.7505 (ptt) REVERT: y 719 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7454 (ttm110) REVERT: y 733 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (ppp) REVERT: y 735 GLU cc_start: 0.8060 (pm20) cc_final: 0.7716 (pm20) REVERT: y 778 MET cc_start: 0.8701 (tmm) cc_final: 0.8457 (tmm) REVERT: y 824 LYS cc_start: 0.8830 (tptp) cc_final: 0.8414 (ttmt) REVERT: y 846 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8309 (mmm-85) REVERT: y 848 GLU cc_start: 0.8023 (pt0) cc_final: 0.7422 (pt0) REVERT: y 859 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7626 (mm) REVERT: G 69 LEU cc_start: 0.8930 (tp) cc_final: 0.8677 (tp) REVERT: K 35 ASN cc_start: 0.8692 (m-40) cc_final: 0.8367 (m-40) REVERT: K 61 ARG cc_start: 0.8777 (ttm110) cc_final: 0.7051 (ttt90) REVERT: K 67 ASP cc_start: 0.9008 (t70) cc_final: 0.8736 (t0) REVERT: M 118 GLN cc_start: 0.8091 (tp40) cc_final: 0.7781 (tp-100) REVERT: L 68 ARG cc_start: 0.6739 (mtt180) cc_final: 0.6516 (mtp180) REVERT: L 72 ASP cc_start: 0.8483 (m-30) cc_final: 0.7546 (p0) REVERT: L 95 ASP cc_start: 0.8414 (m-30) cc_final: 0.7722 (m-30) REVERT: L 178 HIS cc_start: 0.6360 (p90) cc_final: 0.5854 (p90) REVERT: L 216 MET cc_start: 0.8118 (ttm) cc_final: 0.7621 (mtp) REVERT: L 223 TYR cc_start: 0.7596 (m-10) cc_final: 0.7336 (m-10) REVERT: L 256 TRP cc_start: 0.8801 (m-10) cc_final: 0.7039 (m100) REVERT: O 46 LYS cc_start: 0.8495 (mptt) cc_final: 0.8224 (mptt) REVERT: O 110 MET cc_start: 0.8777 (tpp) cc_final: 0.8160 (ttm) REVERT: O 155 TYR cc_start: 0.8700 (m-10) cc_final: 0.8258 (m-80) REVERT: O 182 LYS cc_start: 0.8585 (tttp) cc_final: 0.8230 (ttpt) REVERT: O 209 ASP cc_start: 0.8779 (m-30) cc_final: 0.8462 (m-30) REVERT: N 165 ASN cc_start: 0.8577 (p0) cc_final: 0.8116 (p0) REVERT: Q 95 ARG cc_start: 0.6245 (OUTLIER) cc_final: 0.5889 (mmt180) REVERT: P 76 LEU cc_start: 0.8221 (mt) cc_final: 0.7608 (tt) REVERT: P 80 ASP cc_start: 0.8872 (m-30) cc_final: 0.8304 (m-30) REVERT: P 146 ARG cc_start: 0.4645 (mtt90) cc_final: 0.2999 (ttm170) REVERT: I 70 LYS cc_start: 0.8479 (mtmt) cc_final: 0.7664 (ttpp) REVERT: I 124 ARG cc_start: 0.5462 (mtt180) cc_final: 0.3344 (tmt170) REVERT: I 142 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7210 (tm-30) REVERT: x 44 ASP cc_start: 0.7617 (t0) cc_final: 0.7384 (t70) REVERT: x 71 TYR cc_start: 0.8089 (t80) cc_final: 0.7466 (t80) outliers start: 122 outliers final: 98 residues processed: 651 average time/residue: 0.1891 time to fit residues: 196.2638 Evaluate side-chains 664 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 562 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 19 LEU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 69 GLU Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 259 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 301 HIS Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 501 THR Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 496 THR Chi-restraints excluded: chain y residue 497 GLU Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 546 VAL Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 733 MET Chi-restraints excluded: chain y residue 779 LEU Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 113 GLN Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 267 GLN Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 374 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 398 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 117 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 350 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 109 GLN v 252 HIS v 348 HIS ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 852 GLN x 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130968 restraints weight = 72416.252| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.47 r_work: 0.3602 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31150 Z= 0.147 Angle : 0.597 9.512 42338 Z= 0.312 Chirality : 0.043 0.410 5043 Planarity : 0.004 0.062 5595 Dihedral : 5.931 179.895 4687 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.62 % Favored : 92.35 % Rotamer: Outliers : 4.35 % Allowed : 24.69 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.13), residues: 4356 helix: -0.04 (0.11), residues: 2141 sheet: -2.02 (0.29), residues: 276 loop : -2.23 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 66 TYR 0.031 0.001 TYR N 156 PHE 0.016 0.001 PHE H 47 TRP 0.019 0.001 TRP u 284 HIS 0.012 0.001 HIS v 252 Details of bonding type rmsd covalent geometry : bond 0.00332 (31150) covalent geometry : angle 0.59744 (42338) hydrogen bonds : bond 0.03378 ( 1321) hydrogen bonds : angle 4.60763 ( 3845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 570 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6730 (ttm170) cc_final: 0.5791 (ttm170) REVERT: 6 345 GLN cc_start: 0.6558 (tm-30) cc_final: 0.5567 (mt0) REVERT: u 17 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: u 96 MET cc_start: 0.8438 (tpp) cc_final: 0.7859 (tpt) REVERT: u 105 LYS cc_start: 0.7841 (tppt) cc_final: 0.7558 (tppt) REVERT: u 243 MET cc_start: 0.8834 (tpp) cc_final: 0.8553 (tpp) REVERT: u 318 MET cc_start: 0.6949 (ttt) cc_final: 0.6642 (ttm) REVERT: u 382 TYR cc_start: 0.7145 (m-10) cc_final: 0.6877 (m-10) REVERT: u 398 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6490 (p90) REVERT: u 434 ASN cc_start: 0.8189 (t0) cc_final: 0.7881 (t0) REVERT: v 249 MET cc_start: 0.6372 (mtt) cc_final: 0.6000 (mtt) REVERT: v 368 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7314 (mt-10) REVERT: v 401 TYR cc_start: 0.5728 (t80) cc_final: 0.5483 (m-80) REVERT: y 495 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7958 (m) REVERT: y 648 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8218 (mm-40) REVERT: y 707 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6856 (mmt180) REVERT: y 709 MET cc_start: 0.7979 (ptt) cc_final: 0.7465 (ptt) REVERT: y 733 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7863 (ppp) REVERT: y 758 ASN cc_start: 0.8411 (m-40) cc_final: 0.8145 (m110) REVERT: y 778 MET cc_start: 0.8710 (tmm) cc_final: 0.8459 (tmm) REVERT: y 824 LYS cc_start: 0.8817 (tptp) cc_final: 0.8400 (ttmt) REVERT: y 846 ARG cc_start: 0.8532 (mmm160) cc_final: 0.8115 (mmm-85) REVERT: y 848 GLU cc_start: 0.8060 (pt0) cc_final: 0.7579 (pt0) REVERT: y 859 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7694 (mm) REVERT: G 69 LEU cc_start: 0.8892 (tp) cc_final: 0.8645 (tp) REVERT: K 35 ASN cc_start: 0.8644 (m-40) cc_final: 0.8319 (m-40) REVERT: K 61 ARG cc_start: 0.8755 (ttm110) cc_final: 0.7077 (ttt90) REVERT: K 67 ASP cc_start: 0.8999 (t70) cc_final: 0.8743 (t0) REVERT: M 118 GLN cc_start: 0.8096 (tp40) cc_final: 0.7768 (tp-100) REVERT: L 68 ARG cc_start: 0.6710 (mtt180) cc_final: 0.6498 (mtp180) REVERT: L 72 ASP cc_start: 0.8517 (m-30) cc_final: 0.7616 (p0) REVERT: L 95 ASP cc_start: 0.8401 (m-30) cc_final: 0.7711 (m-30) REVERT: L 178 HIS cc_start: 0.6341 (p90) cc_final: 0.5818 (p90) REVERT: L 216 MET cc_start: 0.8297 (ttm) cc_final: 0.7929 (mtp) REVERT: L 223 TYR cc_start: 0.7592 (m-10) cc_final: 0.7351 (m-10) REVERT: L 256 TRP cc_start: 0.8779 (m-10) cc_final: 0.7069 (m100) REVERT: O 46 LYS cc_start: 0.8483 (mptt) cc_final: 0.8214 (mptt) REVERT: O 110 MET cc_start: 0.8792 (tpp) cc_final: 0.8145 (ttm) REVERT: O 155 TYR cc_start: 0.8691 (m-10) cc_final: 0.8237 (m-80) REVERT: O 182 LYS cc_start: 0.8467 (tttp) cc_final: 0.8104 (ttpt) REVERT: O 209 ASP cc_start: 0.8831 (m-30) cc_final: 0.8591 (m-30) REVERT: N 111 GLN cc_start: 0.8239 (pp30) cc_final: 0.7984 (pp30) REVERT: Q 95 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5757 (mmt180) REVERT: P 76 LEU cc_start: 0.8165 (mt) cc_final: 0.7619 (tt) REVERT: P 80 ASP cc_start: 0.8772 (m-30) cc_final: 0.8220 (m-30) REVERT: P 146 ARG cc_start: 0.4551 (mtt90) cc_final: 0.2916 (ttm170) REVERT: I 70 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7692 (tttt) REVERT: I 124 ARG cc_start: 0.5367 (mtt180) cc_final: 0.3396 (tmt170) REVERT: I 142 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7199 (tm-30) REVERT: x 44 ASP cc_start: 0.7649 (t0) cc_final: 0.7407 (t70) REVERT: x 71 TYR cc_start: 0.8062 (t80) cc_final: 0.7428 (t80) outliers start: 110 outliers final: 89 residues processed: 635 average time/residue: 0.1877 time to fit residues: 191.1646 Evaluate side-chains 657 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 562 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 339 HIS Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 259 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 501 THR Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 356 LEU Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 497 GLU Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 733 MET Chi-restraints excluded: chain y residue 779 LEU Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 144 SER Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 267 GLN Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 77 CYS Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 50 optimal weight: 50.0000 chunk 245 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 400 optimal weight: 30.0000 chunk 301 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 47 optimal weight: 50.0000 chunk 368 optimal weight: 0.0670 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 109 GLN ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN x 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.170325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131339 restraints weight = 73023.371| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.50 r_work: 0.3604 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31150 Z= 0.137 Angle : 0.603 10.560 42338 Z= 0.313 Chirality : 0.043 0.198 5043 Planarity : 0.004 0.062 5595 Dihedral : 5.902 179.387 4687 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.15 % Rotamer: Outliers : 4.12 % Allowed : 24.97 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.13), residues: 4356 helix: 0.00 (0.12), residues: 2143 sheet: -1.98 (0.29), residues: 276 loop : -2.20 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG u 520 TYR 0.029 0.001 TYR N 156 PHE 0.016 0.001 PHE G 173 TRP 0.019 0.001 TRP u 284 HIS 0.007 0.001 HIS v 252 Details of bonding type rmsd covalent geometry : bond 0.00309 (31150) covalent geometry : angle 0.60348 (42338) hydrogen bonds : bond 0.03347 ( 1321) hydrogen bonds : angle 4.58826 ( 3845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 574 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6702 (ttm170) cc_final: 0.5749 (ttm170) REVERT: 6 346 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: u 17 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: u 96 MET cc_start: 0.8432 (tpp) cc_final: 0.7876 (tpt) REVERT: u 105 LYS cc_start: 0.7818 (tppt) cc_final: 0.7554 (tppt) REVERT: u 243 MET cc_start: 0.8844 (tpp) cc_final: 0.8555 (tpp) REVERT: u 318 MET cc_start: 0.7025 (ttt) cc_final: 0.6673 (ttm) REVERT: u 382 TYR cc_start: 0.7167 (m-10) cc_final: 0.6895 (m-10) REVERT: u 398 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.6489 (p90) REVERT: u 434 ASN cc_start: 0.8173 (t0) cc_final: 0.7885 (t0) REVERT: v 249 MET cc_start: 0.6391 (mtt) cc_final: 0.6038 (mtt) REVERT: v 368 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7313 (mt-10) REVERT: v 401 TYR cc_start: 0.5709 (t80) cc_final: 0.5491 (m-80) REVERT: v 403 GLN cc_start: 0.4721 (OUTLIER) cc_final: 0.4477 (mp10) REVERT: y 495 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7943 (m) REVERT: y 648 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8203 (mm-40) REVERT: y 707 ARG cc_start: 0.7094 (mmt180) cc_final: 0.6875 (mmt180) REVERT: y 709 MET cc_start: 0.7993 (ptt) cc_final: 0.7488 (ptt) REVERT: y 719 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7490 (ttm110) REVERT: y 735 GLU cc_start: 0.8035 (pm20) cc_final: 0.7687 (pm20) REVERT: y 758 ASN cc_start: 0.8433 (m-40) cc_final: 0.8163 (m110) REVERT: y 824 LYS cc_start: 0.8814 (tptp) cc_final: 0.8401 (ttmt) REVERT: y 846 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8125 (mmm-85) REVERT: y 848 GLU cc_start: 0.7954 (pt0) cc_final: 0.7476 (pt0) REVERT: G 69 LEU cc_start: 0.8891 (tp) cc_final: 0.8636 (tp) REVERT: K 35 ASN cc_start: 0.8640 (m-40) cc_final: 0.8315 (m-40) REVERT: K 61 ARG cc_start: 0.8701 (ttm110) cc_final: 0.6979 (ttt90) REVERT: K 67 ASP cc_start: 0.8998 (t70) cc_final: 0.8740 (t0) REVERT: M 118 GLN cc_start: 0.8096 (tp40) cc_final: 0.7754 (tp-100) REVERT: L 72 ASP cc_start: 0.8453 (m-30) cc_final: 0.7542 (p0) REVERT: L 94 ILE cc_start: 0.8053 (mm) cc_final: 0.7721 (mm) REVERT: L 95 ASP cc_start: 0.8367 (m-30) cc_final: 0.7711 (m-30) REVERT: L 178 HIS cc_start: 0.6333 (p90) cc_final: 0.5817 (p90) REVERT: L 216 MET cc_start: 0.8295 (ttm) cc_final: 0.7862 (mtp) REVERT: L 223 TYR cc_start: 0.7590 (m-10) cc_final: 0.7355 (m-10) REVERT: L 256 TRP cc_start: 0.8775 (m-10) cc_final: 0.7069 (m100) REVERT: O 46 LYS cc_start: 0.8470 (mptt) cc_final: 0.8193 (mptt) REVERT: O 110 MET cc_start: 0.8767 (tpp) cc_final: 0.8120 (ttm) REVERT: O 113 MET cc_start: 0.8175 (mtm) cc_final: 0.7972 (mtm) REVERT: O 155 TYR cc_start: 0.8591 (m-10) cc_final: 0.8227 (m-80) REVERT: O 182 LYS cc_start: 0.8368 (tttp) cc_final: 0.8014 (ttpt) REVERT: N 111 GLN cc_start: 0.8221 (pp30) cc_final: 0.7964 (pp30) REVERT: Q 95 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5777 (mmt180) REVERT: P 76 LEU cc_start: 0.8172 (mt) cc_final: 0.7618 (tt) REVERT: P 80 ASP cc_start: 0.8760 (m-30) cc_final: 0.8207 (m-30) REVERT: P 146 ARG cc_start: 0.4601 (mtt90) cc_final: 0.2969 (ttm170) REVERT: I 70 LYS cc_start: 0.8454 (mtmt) cc_final: 0.7685 (tttt) REVERT: I 103 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8110 (mm-30) REVERT: I 124 ARG cc_start: 0.5319 (mtt180) cc_final: 0.3373 (tmt170) REVERT: I 142 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7184 (tm-30) REVERT: x 44 ASP cc_start: 0.7649 (t0) cc_final: 0.7403 (t70) REVERT: x 71 TYR cc_start: 0.8033 (t80) cc_final: 0.7398 (t80) outliers start: 104 outliers final: 91 residues processed: 640 average time/residue: 0.1921 time to fit residues: 196.5217 Evaluate side-chains 653 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 556 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 346 GLN Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 259 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 501 THR Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 356 LEU Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain v residue 403 GLN Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 496 THR Chi-restraints excluded: chain y residue 497 GLU Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 698 MET Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 779 LEU Chi-restraints excluded: chain y residue 807 LEU Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 267 GLN Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 107 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 431 optimal weight: 50.0000 chunk 187 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 chunk 248 optimal weight: 0.5980 chunk 432 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 336 HIS ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 109 GLN v 231 ASN ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.169256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.131999 restraints weight = 84413.439| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 4.06 r_work: 0.3575 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 31150 Z= 0.182 Angle : 0.710 59.199 42338 Z= 0.389 Chirality : 0.045 0.782 5043 Planarity : 0.004 0.062 5595 Dihedral : 5.897 179.348 4687 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 4.31 % Allowed : 24.89 % Favored : 70.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.13), residues: 4356 helix: -0.01 (0.11), residues: 2143 sheet: -1.97 (0.29), residues: 276 loop : -2.21 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG x 26 TYR 0.026 0.001 TYR N 156 PHE 0.016 0.001 PHE H 47 TRP 0.018 0.001 TRP u 284 HIS 0.006 0.001 HIS v 252 Details of bonding type rmsd covalent geometry : bond 0.00408 (31150) covalent geometry : angle 0.70980 (42338) hydrogen bonds : bond 0.03350 ( 1321) hydrogen bonds : angle 4.58720 ( 3845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8712 Ramachandran restraints generated. 4356 Oldfield, 0 Emsley, 4356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 555 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 330 ARG cc_start: 0.6754 (ttm170) cc_final: 0.5792 (ttm170) REVERT: 6 345 GLN cc_start: 0.6376 (tm-30) cc_final: 0.5167 (mt0) REVERT: u 17 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: u 96 MET cc_start: 0.8461 (tpp) cc_final: 0.7913 (tpt) REVERT: u 105 LYS cc_start: 0.7823 (tppt) cc_final: 0.7567 (tppt) REVERT: u 243 MET cc_start: 0.8866 (tpp) cc_final: 0.8590 (tpp) REVERT: u 306 MET cc_start: 0.7295 (ppp) cc_final: 0.6983 (ppp) REVERT: u 318 MET cc_start: 0.7014 (ttt) cc_final: 0.6679 (ttm) REVERT: u 382 TYR cc_start: 0.7191 (m-10) cc_final: 0.6923 (m-10) REVERT: u 398 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6509 (p90) REVERT: u 434 ASN cc_start: 0.8205 (t0) cc_final: 0.7919 (t0) REVERT: v 249 MET cc_start: 0.6425 (mtt) cc_final: 0.6085 (mtt) REVERT: v 368 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7314 (mt-10) REVERT: v 401 TYR cc_start: 0.5735 (t80) cc_final: 0.5500 (m-80) REVERT: v 403 GLN cc_start: 0.4710 (OUTLIER) cc_final: 0.4469 (mp10) REVERT: y 459 MET cc_start: 0.8782 (mmm) cc_final: 0.8049 (mmm) REVERT: y 495 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (m) REVERT: y 648 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8221 (mm-40) REVERT: y 707 ARG cc_start: 0.7084 (mmt180) cc_final: 0.6862 (mmt180) REVERT: y 709 MET cc_start: 0.8012 (ptt) cc_final: 0.7491 (ptt) REVERT: y 719 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7517 (ttm110) REVERT: y 735 GLU cc_start: 0.8034 (pm20) cc_final: 0.7769 (pm20) REVERT: y 758 ASN cc_start: 0.8480 (m-40) cc_final: 0.8223 (m110) REVERT: y 778 MET cc_start: 0.8641 (tmm) cc_final: 0.8424 (tmm) REVERT: y 824 LYS cc_start: 0.8823 (tptp) cc_final: 0.8411 (ttmt) REVERT: y 846 ARG cc_start: 0.8569 (mmm160) cc_final: 0.8156 (mmm-85) REVERT: y 848 GLU cc_start: 0.7962 (pt0) cc_final: 0.7480 (pt0) REVERT: y 859 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7729 (mm) REVERT: G 69 LEU cc_start: 0.8904 (tp) cc_final: 0.8651 (tp) REVERT: K 35 ASN cc_start: 0.8657 (m-40) cc_final: 0.8338 (m-40) REVERT: K 61 ARG cc_start: 0.8709 (ttm110) cc_final: 0.6983 (ttt90) REVERT: K 67 ASP cc_start: 0.9024 (t70) cc_final: 0.8773 (t0) REVERT: M 118 GLN cc_start: 0.8106 (tp40) cc_final: 0.7768 (tp-100) REVERT: L 72 ASP cc_start: 0.8470 (m-30) cc_final: 0.7560 (p0) REVERT: L 94 ILE cc_start: 0.8073 (mm) cc_final: 0.7751 (mm) REVERT: L 95 ASP cc_start: 0.8392 (m-30) cc_final: 0.7725 (m-30) REVERT: L 178 HIS cc_start: 0.6341 (p90) cc_final: 0.5826 (p90) REVERT: L 216 MET cc_start: 0.8296 (ttm) cc_final: 0.7872 (mtp) REVERT: L 223 TYR cc_start: 0.7617 (m-10) cc_final: 0.7386 (m-10) REVERT: L 256 TRP cc_start: 0.8798 (m-10) cc_final: 0.7082 (m100) REVERT: O 46 LYS cc_start: 0.8466 (mptt) cc_final: 0.8198 (mptt) REVERT: O 110 MET cc_start: 0.8821 (tpp) cc_final: 0.8171 (ttm) REVERT: O 155 TYR cc_start: 0.8615 (m-10) cc_final: 0.8194 (m-80) REVERT: O 182 LYS cc_start: 0.8406 (tttp) cc_final: 0.8050 (ttpt) REVERT: N 111 GLN cc_start: 0.8237 (pp30) cc_final: 0.7980 (pp30) REVERT: Q 95 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5855 (mmt180) REVERT: P 76 LEU cc_start: 0.8191 (mt) cc_final: 0.7637 (tt) REVERT: P 80 ASP cc_start: 0.8785 (m-30) cc_final: 0.8241 (m-30) REVERT: P 146 ARG cc_start: 0.4690 (mtt90) cc_final: 0.2981 (ttm170) REVERT: I 70 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7692 (tttm) REVERT: I 103 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8186 (mm-30) REVERT: I 124 ARG cc_start: 0.5388 (mtt180) cc_final: 0.3382 (tmt170) REVERT: I 142 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7190 (tm-30) REVERT: x 44 ASP cc_start: 0.7693 (t0) cc_final: 0.7438 (t70) REVERT: x 71 TYR cc_start: 0.8067 (t80) cc_final: 0.7425 (t80) outliers start: 109 outliers final: 97 residues processed: 624 average time/residue: 0.1948 time to fit residues: 194.1209 Evaluate side-chains 654 residues out of total 3931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 551 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 333 VAL Chi-restraints excluded: chain 6 residue 336 HIS Chi-restraints excluded: chain u residue 17 GLU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain u residue 59 VAL Chi-restraints excluded: chain u residue 69 GLU Chi-restraints excluded: chain u residue 109 GLN Chi-restraints excluded: chain u residue 112 VAL Chi-restraints excluded: chain u residue 184 PHE Chi-restraints excluded: chain u residue 228 MET Chi-restraints excluded: chain u residue 230 LEU Chi-restraints excluded: chain u residue 237 LEU Chi-restraints excluded: chain u residue 259 LEU Chi-restraints excluded: chain u residue 296 LEU Chi-restraints excluded: chain u residue 337 ASP Chi-restraints excluded: chain u residue 342 LEU Chi-restraints excluded: chain u residue 343 ASP Chi-restraints excluded: chain u residue 398 PHE Chi-restraints excluded: chain u residue 407 VAL Chi-restraints excluded: chain u residue 408 THR Chi-restraints excluded: chain u residue 450 ILE Chi-restraints excluded: chain u residue 452 PHE Chi-restraints excluded: chain u residue 462 VAL Chi-restraints excluded: chain u residue 471 ILE Chi-restraints excluded: chain u residue 501 THR Chi-restraints excluded: chain u residue 527 SER Chi-restraints excluded: chain v residue 236 PHE Chi-restraints excluded: chain v residue 247 GLN Chi-restraints excluded: chain v residue 301 VAL Chi-restraints excluded: chain v residue 315 CYS Chi-restraints excluded: chain v residue 322 ASP Chi-restraints excluded: chain v residue 326 VAL Chi-restraints excluded: chain v residue 343 THR Chi-restraints excluded: chain v residue 356 LEU Chi-restraints excluded: chain v residue 392 VAL Chi-restraints excluded: chain v residue 403 GLN Chi-restraints excluded: chain y residue 444 ILE Chi-restraints excluded: chain y residue 495 THR Chi-restraints excluded: chain y residue 496 THR Chi-restraints excluded: chain y residue 497 GLU Chi-restraints excluded: chain y residue 499 VAL Chi-restraints excluded: chain y residue 596 ASP Chi-restraints excluded: chain y residue 614 VAL Chi-restraints excluded: chain y residue 666 GLU Chi-restraints excluded: chain y residue 695 ILE Chi-restraints excluded: chain y residue 720 VAL Chi-restraints excluded: chain y residue 779 LEU Chi-restraints excluded: chain y residue 792 LEU Chi-restraints excluded: chain y residue 852 GLN Chi-restraints excluded: chain y residue 859 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain M residue 83 ASN Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain L residue 60 TRP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 215 MET Chi-restraints excluded: chain L residue 252 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 267 GLN Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 78 GLU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 111 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 178 THR Chi-restraints excluded: chain O residue 210 VAL Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 141 ASN Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 62 VAL Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 133 ARG Chi-restraints excluded: chain x residue 39 LEU Chi-restraints excluded: chain x residue 42 VAL Chi-restraints excluded: chain x residue 69 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 153 optimal weight: 7.9990 chunk 415 optimal weight: 20.0000 chunk 97 optimal weight: 0.0170 chunk 84 optimal weight: 6.9990 chunk 392 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 416 optimal weight: 9.9990 chunk 281 optimal weight: 0.2980 chunk 426 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 109 GLN ** y 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** O 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.170067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132522 restraints weight = 84715.572| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.99 r_work: 0.3579 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 31150 Z= 0.182 Angle : 0.699 47.522 42338 Z= 0.393 Chirality : 0.045 0.782 5043 Planarity : 0.004 0.062 5595 Dihedral : 5.897 179.348 4687 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 4.12 % Allowed : 25.09 % Favored : 70.80 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.13), residues: 4356 helix: -0.01 (0.11), residues: 2143 sheet: -1.97 (0.29), residues: 276 loop : -2.21 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG x 26 TYR 0.026 0.001 TYR N 156 PHE 0.016 0.001 PHE H 47 TRP 0.018 0.001 TRP u 284 HIS 0.006 0.001 HIS v 252 Details of bonding type rmsd covalent geometry : bond 0.00409 (31150) covalent geometry : angle 0.69924 (42338) hydrogen bonds : bond 0.03350 ( 1321) hydrogen bonds : angle 4.58720 ( 3845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13009.66 seconds wall clock time: 221 minutes 20.17 seconds (13280.17 seconds total)