Starting phenix.real_space_refine on Sat Jan 18 11:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzv_38799/01_2025/8xzv_38799.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 284 5.16 5 C 37405 2.51 5 N 10320 2.21 5 O 10989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 58999 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1775 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "B" Number of atoms: 8517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8517 Classifications: {'peptide': 1070} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1021} Chain: "C" Number of atoms: 5507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5507 Classifications: {'peptide': 677} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 642} Chain: "D" Number of atoms: 8374 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1216, 8370 Classifications: {'peptide': 1216} Incomplete info: {'truncation_to_alanine': 379} Link IDs: {'PTRANS': 47, 'TRANS': 1168} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1443 Unresolved non-hydrogen angles: 1837 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 26, 'TRP:plan': 4, 'ASP:plan': 18, 'PHE:plan': 27, 'GLU:plan': 21, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 786 Conformer: "B" Number of residues, atoms: 1216, 8370 Classifications: {'peptide': 1216} Incomplete info: {'truncation_to_alanine': 379} Link IDs: {'PTRANS': 47, 'TRANS': 1168} Chain breaks: 2 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1443 Unresolved non-hydrogen angles: 1837 Unresolved non-hydrogen dihedrals: 1222 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 26, 'TRP:plan': 4, 'ASP:plan': 18, 'PHE:plan': 27, 'GLU:plan': 21, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 786 bond proxies already assigned to first conformer: 8488 Chain: "E" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3079 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 362} Chain: "F" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 2009 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 16, 'TRANS': 220} Chain: "H" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4653 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 23, 'TRANS': 571} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "I" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3373 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 392} Chain: "K" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1803 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 197} Chain: "L" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1817 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 15, 'TRANS': 208} Chain: "M" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1763 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "N" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 4032 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 445} Chain: "O" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1761 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "P" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 840 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "Q" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 902 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "R" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 940 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "S" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2695 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 17, 'TRANS': 326} Chain: "J" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4218 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 521} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 302 residue: pdb=" N LYS D 562 " occ=0.00 ... (3 atoms not shown) pdb=" CB LYS D 562 " occ=0.00 residue: pdb=" N ARG D 563 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG D 563 " occ=0.00 residue: pdb=" N ARG D 564 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG D 564 " occ=0.00 residue: pdb=" N ASN D 565 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASN D 565 " occ=0.00 residue: pdb=" N ARG D 566 " occ=0.00 ... (3 atoms not shown) pdb=" CB ARG D 566 " occ=0.00 residue: pdb=" N PHE D 567 " occ=0.00 ... (3 atoms not shown) pdb=" CB PHE D 567 " occ=0.00 residue: pdb=" N ILE D 568 " occ=0.00 ... (3 atoms not shown) pdb=" CB ILE D 568 " occ=0.00 residue: pdb=" N ILE D 569 " occ=0.00 ... (3 atoms not shown) pdb=" CB ILE D 569 " occ=0.00 residue: pdb=" N PRO D 570 " occ=0.00 ... (3 atoms not shown) pdb=" CB PRO D 570 " occ=0.00 residue: pdb=" N PHE D 571 " occ=0.00 ... (3 atoms not shown) pdb=" CB PHE D 571 " occ=0.00 residue: pdb=" N GLN D 572 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN D 572 " occ=0.00 residue: pdb=" N GLY D 573 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY D 573 " occ=0.00 ... (remaining 290 not shown) Time building chain proxies: 26.62, per 1000 atoms: 0.45 Number of scatterers: 58999 At special positions: 0 Unit cell: (163.9, 231, 247.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 284 16.00 O 10989 8.00 N 10320 7.00 C 37405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 104 " - pdb=" SG CYS F 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 107 " distance=2.03 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: 10.70 Conformation dependent library (CDL) restraints added in 6.9 seconds 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14026 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 77 sheets defined 36.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 removed outlier: 3.512A pdb=" N THR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'B' and resid 16 through 36 removed outlier: 4.699A pdb=" N LEU B 31 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.747A pdb=" N ASN B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.899A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS B 250 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 282 through 298 removed outlier: 3.503A pdb=" N ILE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 316 through 343 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 359 through 372 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.576A pdb=" N GLN B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 387 " --> pdb=" O PRO B 383 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 391 " --> pdb=" O ILE B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 470 through 475 removed outlier: 4.040A pdb=" N GLU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 494 removed outlier: 3.586A pdb=" N GLU B 494 " --> pdb=" O ILE B 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 491 through 494' Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.548A pdb=" N LEU B 530 " --> pdb=" O GLY B 527 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 531 " --> pdb=" O ALA B 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 527 through 531' Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.597A pdb=" N ALA B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N MET B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 576 removed outlier: 4.410A pdb=" N GLY B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 680 removed outlier: 3.656A pdb=" N GLU B 680 " --> pdb=" O ARG B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.791A pdb=" N MET B 839 " --> pdb=" O ARG B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 861 removed outlier: 3.659A pdb=" N SER B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 877 removed outlier: 3.662A pdb=" N PHE B 867 " --> pdb=" O VAL B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 911 Processing helix chain 'B' and resid 953 through 957 Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 998 through 1005 removed outlier: 3.910A pdb=" N LEU B1002 " --> pdb=" O VAL B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1025 removed outlier: 3.551A pdb=" N ARG B1016 " --> pdb=" O HIS B1012 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B1018 " --> pdb=" O LYS B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1048 removed outlier: 3.522A pdb=" N ARG B1040 " --> pdb=" O PRO B1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 25 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.788A pdb=" N ILE C 99 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 3.887A pdb=" N ARG C 121 " --> pdb=" O TRP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 131 removed outlier: 3.681A pdb=" N ASN C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.547A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 removed outlier: 3.519A pdb=" N LYS C 172 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.094A pdb=" N PHE C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'C' and resid 195 through 204 removed outlier: 4.037A pdb=" N ILE C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 224 Processing helix chain 'C' and resid 230 through 256 removed outlier: 3.829A pdb=" N VAL C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 263 Processing helix chain 'C' and resid 290 through 312 removed outlier: 3.579A pdb=" N GLU C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 337 removed outlier: 3.847A pdb=" N MET C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.531A pdb=" N ILE C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 399 through 404' Processing helix chain 'C' and resid 406 through 417 Processing helix chain 'C' and resid 422 through 432 Processing helix chain 'C' and resid 434 through 441 removed outlier: 4.111A pdb=" N TRP C 438 " --> pdb=" O GLU C 434 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 532 through 543 Processing helix chain 'C' and resid 583 through 593 Processing helix chain 'C' and resid 655 through 676 removed outlier: 3.680A pdb=" N GLN C 674 " --> pdb=" O GLN C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 31 Processing helix chain 'D' and resid 33 through 53 removed outlier: 4.154A pdb=" N HIS D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 86 removed outlier: 3.758A pdb=" N GLN D 73 " --> pdb=" O GLY D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.545A pdb=" N ILE D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TRP D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 139 through 147 removed outlier: 3.730A pdb=" N LEU D 146 " --> pdb=" O GLN D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 187 removed outlier: 3.790A pdb=" N TYR D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 210 removed outlier: 3.682A pdb=" N ALA D 199 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 removed outlier: 3.691A pdb=" N ASN D 232 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 233 " --> pdb=" O PRO D 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 229 through 233' Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.729A pdb=" N GLN D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 277 removed outlier: 4.106A pdb=" N VAL D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.625A pdb=" N CYS D 291 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.697A pdb=" N LEU D 366 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL D 367 " --> pdb=" O GLU D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 486 through 490 Processing helix chain 'D' and resid 502 through 509 removed outlier: 3.816A pdb=" N ILE D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 987 Processing helix chain 'D' and resid 1129 through 1138 Processing helix chain 'D' and resid 1148 through 1160 Processing helix chain 'D' and resid 1165 through 1195 removed outlier: 3.684A pdb=" N LEU D1171 " --> pdb=" O PRO D1167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D1187 " --> pdb=" O ILE D1183 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D1192 " --> pdb=" O LYS D1188 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR D1193 " --> pdb=" O ILE D1189 " (cutoff:3.500A) Processing helix chain 'D' and resid 1201 through 1213 removed outlier: 4.111A pdb=" N ILE D1205 " --> pdb=" O HIS D1201 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D1208 " --> pdb=" O HIS D1204 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D1211 " --> pdb=" O ILE D1207 " (cutoff:3.500A) Processing helix chain 'D' and resid 1234 through 1243 removed outlier: 3.775A pdb=" N THR D1241 " --> pdb=" O ARG D1237 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D1243 " --> pdb=" O GLU D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1259 through 1264 Processing helix chain 'D' and resid 1267 through 1273 removed outlier: 3.683A pdb=" N GLU D1271 " --> pdb=" O SER D1267 " (cutoff:3.500A) Processing helix chain 'D' and resid 1276 through 1288 Processing helix chain 'D' and resid 1296 through 1302 Processing helix chain 'D' and resid 1308 through 1312 removed outlier: 3.618A pdb=" N PHE D1312 " --> pdb=" O GLY D1309 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.870A pdb=" N GLY E 132 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.650A pdb=" N TRP E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN E 139 " --> pdb=" O MET E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.622A pdb=" N VAL E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 186 removed outlier: 3.504A pdb=" N VAL E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.724A pdb=" N LEU E 235 " --> pdb=" O ALA E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 251 through 254 Processing helix chain 'E' and resid 255 through 272 removed outlier: 3.626A pdb=" N THR E 260 " --> pdb=" O PRO E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.530A pdb=" N LYS E 288 " --> pdb=" O PRO E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 302 removed outlier: 4.904A pdb=" N GLN E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 removed outlier: 3.801A pdb=" N LEU E 317 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 328 removed outlier: 3.684A pdb=" N LYS E 327 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 328 " --> pdb=" O GLU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 403 through 419 Processing helix chain 'E' and resid 421 through 424 removed outlier: 3.755A pdb=" N GLU E 424 " --> pdb=" O GLU E 421 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 421 through 424' Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 433 through 443 removed outlier: 3.730A pdb=" N ILE E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 467 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.705A pdb=" N VAL F 119 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.506A pdb=" N ALA F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'G' and resid 193 through 198 Processing helix chain 'G' and resid 234 through 238 removed outlier: 4.516A pdb=" N ARG G 238 " --> pdb=" O ARG G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 253 removed outlier: 3.587A pdb=" N LYS G 249 " --> pdb=" O THR G 245 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU G 253 " --> pdb=" O LYS G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 273 removed outlier: 3.773A pdb=" N SER G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 295 removed outlier: 3.758A pdb=" N PHE G 279 " --> pdb=" O ARG G 275 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 291 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU G 292 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 293 " --> pdb=" O GLU G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 314 through 323 removed outlier: 3.829A pdb=" N LYS G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 335 Processing helix chain 'G' and resid 339 through 347 Processing helix chain 'G' and resid 348 through 350 No H-bonds generated for 'chain 'G' and resid 348 through 350' Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.606A pdb=" N ARG G 361 " --> pdb=" O LEU G 358 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET G 362 " --> pdb=" O ALA G 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 358 through 362' Processing helix chain 'G' and resid 363 through 369 Processing helix chain 'G' and resid 378 through 381 removed outlier: 3.545A pdb=" N ASN G 381 " --> pdb=" O PRO G 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 378 through 381' Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 414 through 422 Processing helix chain 'H' and resid 64 through 78 removed outlier: 3.808A pdb=" N VAL H 72 " --> pdb=" O GLY H 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE H 73 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU H 76 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET H 78 " --> pdb=" O MET H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 86 through 99 removed outlier: 3.934A pdb=" N SER H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET H 96 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 99 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 117 removed outlier: 3.914A pdb=" N LEU H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL H 112 " --> pdb=" O TYR H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 135 removed outlier: 3.532A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 154 Processing helix chain 'H' and resid 156 through 167 removed outlier: 4.309A pdb=" N LEU H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET H 166 " --> pdb=" O ILE H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 189 through 203 removed outlier: 4.265A pdb=" N GLY H 203 " --> pdb=" O LYS H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 224 through 238 removed outlier: 3.588A pdb=" N ALA H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 256 removed outlier: 4.175A pdb=" N VAL H 253 " --> pdb=" O CYS H 249 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 272 removed outlier: 3.942A pdb=" N THR H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 293 removed outlier: 3.506A pdb=" N ASN H 285 " --> pdb=" O THR H 281 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG H 293 " --> pdb=" O GLN H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 313 removed outlier: 3.654A pdb=" N VAL H 303 " --> pdb=" O ARG H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 334 removed outlier: 3.514A pdb=" N HIS H 324 " --> pdb=" O ASN H 320 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR H 334 " --> pdb=" O CYS H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 349 removed outlier: 3.758A pdb=" N HIS H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA H 346 " --> pdb=" O ARG H 342 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 359 Processing helix chain 'H' and resid 365 through 378 Processing helix chain 'H' and resid 380 through 394 removed outlier: 3.550A pdb=" N LYS H 392 " --> pdb=" O GLU H 388 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP H 393 " --> pdb=" O THR H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 402 Processing helix chain 'H' and resid 433 through 437 removed outlier: 3.665A pdb=" N ILE H 436 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 495 removed outlier: 4.178A pdb=" N LEU H 489 " --> pdb=" O ARG H 485 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS H 492 " --> pdb=" O LYS H 488 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 493 " --> pdb=" O LEU H 489 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 519 removed outlier: 3.734A pdb=" N VAL H 513 " --> pdb=" O ASP H 509 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS H 519 " --> pdb=" O GLU H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 760 Processing helix chain 'H' and resid 763 through 771 removed outlier: 5.764A pdb=" N GLU H 768 " --> pdb=" O TRP H 765 " (cutoff:3.500A) Processing helix chain 'H' and resid 784 through 795 Processing helix chain 'H' and resid 801 through 805 Processing helix chain 'H' and resid 807 through 812 Processing helix chain 'H' and resid 823 through 827 removed outlier: 4.191A pdb=" N THR H 827 " --> pdb=" O ILE H 824 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 87 removed outlier: 4.074A pdb=" N TYR I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 93 Processing helix chain 'I' and resid 155 through 161 Processing helix chain 'I' and resid 167 through 179 removed outlier: 4.646A pdb=" N ARG I 171 " --> pdb=" O ASP I 167 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU I 172 " --> pdb=" O TRP I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 191 removed outlier: 3.695A pdb=" N LEU I 189 " --> pdb=" O ASN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 207 through 213 Processing helix chain 'I' and resid 217 through 228 Processing helix chain 'I' and resid 231 through 236 removed outlier: 3.551A pdb=" N LYS I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 266 Processing helix chain 'I' and resid 367 through 372 removed outlier: 3.943A pdb=" N PHE I 372 " --> pdb=" O PHE I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 403 Processing helix chain 'I' and resid 426 through 436 Processing helix chain 'I' and resid 446 through 450 Processing helix chain 'I' and resid 462 through 487 Processing helix chain 'K' and resid 276 through 279 Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 291 through 313 removed outlier: 3.632A pdb=" N ASP K 307 " --> pdb=" O ARG K 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 70 Processing helix chain 'L' and resid 74 through 85 removed outlier: 3.624A pdb=" N PHE L 78 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY L 83 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS L 85 " --> pdb=" O HIS L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 97 Processing helix chain 'L' and resid 106 through 110 removed outlier: 4.155A pdb=" N GLU L 109 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL L 110 " --> pdb=" O LEU L 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 106 through 110' Processing helix chain 'L' and resid 123 through 139 removed outlier: 3.953A pdb=" N GLN L 129 " --> pdb=" O ASN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 160 Processing helix chain 'L' and resid 162 through 176 removed outlier: 3.594A pdb=" N THR L 167 " --> pdb=" O PHE L 163 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR L 168 " --> pdb=" O GLU L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 223 Processing helix chain 'L' and resid 234 through 237 Processing helix chain 'L' and resid 238 through 243 Processing helix chain 'L' and resid 245 through 257 removed outlier: 3.791A pdb=" N TYR L 249 " --> pdb=" O ARG L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 279 removed outlier: 3.674A pdb=" N VAL L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 87 Processing helix chain 'M' and resid 87 through 103 removed outlier: 3.830A pdb=" N ARG M 102 " --> pdb=" O ARG M 98 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER M 103 " --> pdb=" O HIS M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 119 Processing helix chain 'M' and resid 127 through 143 Processing helix chain 'M' and resid 155 through 164 removed outlier: 3.571A pdb=" N GLN M 159 " --> pdb=" O GLY M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 180 Processing helix chain 'M' and resid 208 through 213 removed outlier: 3.619A pdb=" N TRP M 212 " --> pdb=" O PRO M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 246 removed outlier: 4.294A pdb=" N TYR M 238 " --> pdb=" O ASP M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 260 Processing helix chain 'N' and resid 78 through 86 Processing helix chain 'N' and resid 97 through 107 removed outlier: 3.761A pdb=" N ALA N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG N 104 " --> pdb=" O ALA N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 126 Processing helix chain 'N' and resid 128 through 140 Processing helix chain 'N' and resid 147 through 151 removed outlier: 3.779A pdb=" N GLN N 150 " --> pdb=" O TYR N 147 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE N 151 " --> pdb=" O ALA N 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 151' Processing helix chain 'N' and resid 187 through 195 Processing helix chain 'N' and resid 195 through 200 Processing helix chain 'N' and resid 223 through 251 removed outlier: 5.720A pdb=" N ASP N 241 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS N 242 " --> pdb=" O PHE N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 265 removed outlier: 3.625A pdb=" N ASP N 264 " --> pdb=" O ARG N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 275 Processing helix chain 'N' and resid 309 through 311 No H-bonds generated for 'chain 'N' and resid 309 through 311' Processing helix chain 'N' and resid 312 through 317 Processing helix chain 'N' and resid 373 through 382 removed outlier: 3.948A pdb=" N ARG N 378 " --> pdb=" O LEU N 374 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG N 379 " --> pdb=" O ASP N 375 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 422 removed outlier: 4.013A pdb=" N GLN N 412 " --> pdb=" O ASP N 408 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 432 removed outlier: 3.521A pdb=" N TYR N 431 " --> pdb=" O PRO N 428 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS N 432 " --> pdb=" O ASP N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 471 through 475 Processing helix chain 'N' and resid 476 through 498 removed outlier: 4.398A pdb=" N ALA N 480 " --> pdb=" O ASP N 476 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN N 485 " --> pdb=" O PHE N 481 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU N 495 " --> pdb=" O GLN N 491 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU N 496 " --> pdb=" O LYS N 492 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG N 497 " --> pdb=" O GLU N 493 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 541 removed outlier: 3.773A pdb=" N ASP N 513 " --> pdb=" O ASN N 509 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU N 531 " --> pdb=" O ARG N 527 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG N 532 " --> pdb=" O GLU N 528 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER N 535 " --> pdb=" O LEU N 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 55 removed outlier: 3.703A pdb=" N THR O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY O 55 " --> pdb=" O ARG O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 91 Processing helix chain 'O' and resid 119 through 121 No H-bonds generated for 'chain 'O' and resid 119 through 121' Processing helix chain 'O' and resid 212 through 227 removed outlier: 3.899A pdb=" N LEU O 222 " --> pdb=" O ALA O 218 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU O 225 " --> pdb=" O ASN O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 228 through 231 Processing helix chain 'P' and resid 78 through 87 removed outlier: 3.876A pdb=" N ARG P 82 " --> pdb=" O GLU P 78 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS P 83 " --> pdb=" O GLU P 79 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL P 84 " --> pdb=" O GLN P 80 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN P 85 " --> pdb=" O MET P 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 99 removed outlier: 3.592A pdb=" N ASP P 96 " --> pdb=" O ALA P 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG P 97 " --> pdb=" O GLY P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 123 Processing helix chain 'P' and resid 124 through 127 Processing helix chain 'P' and resid 131 through 142 Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'Q' and resid 39 through 44 removed outlier: 4.000A pdb=" N TYR Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 61 removed outlier: 3.839A pdb=" N LEU Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN Q 58 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU Q 59 " --> pdb=" O GLU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'R' and resid 80 through 85 removed outlier: 3.564A pdb=" N THR R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 121 removed outlier: 3.795A pdb=" N GLU R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 169 through 180 removed outlier: 3.629A pdb=" N ASP R 175 " --> pdb=" O GLN R 171 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU R 177 " --> pdb=" O MET R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.743A pdb=" N LEU S 234 " --> pdb=" O LYS S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 249 through 259 removed outlier: 4.290A pdb=" N ILE S 253 " --> pdb=" O GLY S 249 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA S 254 " --> pdb=" O GLY S 250 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU S 258 " --> pdb=" O ALA S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 271 through 284 Processing helix chain 'S' and resid 345 through 349 Processing helix chain 'S' and resid 350 through 360 removed outlier: 3.842A pdb=" N ARG S 354 " --> pdb=" O ASP S 350 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS S 355 " --> pdb=" O ALA S 351 " (cutoff:3.500A) Processing helix chain 'S' and resid 360 through 367 removed outlier: 4.122A pdb=" N LEU S 367 " --> pdb=" O ILE S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 384 through 390 removed outlier: 3.937A pdb=" N THR S 388 " --> pdb=" O SER S 384 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER S 390 " --> pdb=" O GLU S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 398 removed outlier: 4.249A pdb=" N LEU S 398 " --> pdb=" O VAL S 395 " (cutoff:3.500A) Processing helix chain 'S' and resid 406 through 411 Processing helix chain 'S' and resid 435 through 439 Processing helix chain 'S' and resid 487 through 503 removed outlier: 3.583A pdb=" N VAL S 493 " --> pdb=" O GLY S 489 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU S 496 " --> pdb=" O LEU S 492 " (cutoff:3.500A) Processing helix chain 'S' and resid 509 through 529 removed outlier: 3.943A pdb=" N SER S 516 " --> pdb=" O TYR S 512 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP S 529 " --> pdb=" O VAL S 525 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 254 Processing helix chain 'J' and resid 275 through 279 Processing helix chain 'J' and resid 293 through 302 removed outlier: 3.734A pdb=" N GLU J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 341 Proline residue: J 334 - end of helix Processing helix chain 'J' and resid 358 through 373 Processing helix chain 'J' and resid 401 through 415 removed outlier: 3.541A pdb=" N VAL J 405 " --> pdb=" O ASP J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 431 Processing helix chain 'J' and resid 433 through 437 removed outlier: 3.556A pdb=" N GLU J 436 " --> pdb=" O ARG J 433 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE J 437 " --> pdb=" O CYS J 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 433 through 437' Processing helix chain 'J' and resid 457 through 465 Processing helix chain 'J' and resid 466 through 471 Processing helix chain 'J' and resid 488 through 495 removed outlier: 3.741A pdb=" N GLN J 495 " --> pdb=" O PHE J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 562 Processing helix chain 'J' and resid 565 through 575 Processing helix chain 'J' and resid 601 through 615 removed outlier: 3.768A pdb=" N LEU J 605 " --> pdb=" O THR J 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 634 through 646 Processing helix chain 'J' and resid 660 through 668 Processing helix chain 'J' and resid 676 through 681 Processing helix chain 'J' and resid 691 through 694 No H-bonds generated for 'chain 'J' and resid 691 through 694' Processing helix chain 'J' and resid 702 through 714 removed outlier: 4.117A pdb=" N GLY J 714 " --> pdb=" O ALA J 710 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 757 removed outlier: 4.689A pdb=" N ASP J 754 " --> pdb=" O LEU J 750 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU J 755 " --> pdb=" O GLN J 751 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 24 removed outlier: 6.597A pdb=" N ARG A 31 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 20 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR A 29 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N THR A 22 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU A 27 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU A 197 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 110 removed outlier: 3.664A pdb=" N ARG A 64 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A 152 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE A 62 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASN A 154 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR A 60 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.944A pdb=" N GLY A 156 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 176 " --> pdb=" O GLY A 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.870A pdb=" N GLY B 102 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 82 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 100 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AA9, first strand: chain 'B' and resid 312 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.969A pdb=" N TYR B 146 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 162 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 443 through 444 Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 444 Processing sheet with id=AB4, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AB5, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB6, first strand: chain 'B' and resid 579 through 580 removed outlier: 6.818A pdb=" N ALA B 579 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 623 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 586 through 591 removed outlier: 5.684A pdb=" N ILE B 587 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 598 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 653 through 654 Processing sheet with id=AB9, first strand: chain 'B' and resid 829 through 834 removed outlier: 7.624A pdb=" N VAL B 671 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 833 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 673 " --> pdb=" O ILE B 833 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE B 941 " --> pdb=" O TYR B 659 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 685 through 693 removed outlier: 3.713A pdb=" N ASP B 787 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 809 " --> pdb=" O VAL B 785 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B 785 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N LYS B 811 " --> pdb=" O GLY B 783 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLY B 783 " --> pdb=" O LYS B 811 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 704 through 705 removed outlier: 3.678A pdb=" N LYS B 704 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 743 " --> pdb=" O LYS B 771 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 704 through 705 removed outlier: 3.678A pdb=" N LYS B 704 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B 739 " --> pdb=" O LEU B 775 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 984 through 985 removed outlier: 3.542A pdb=" N VAL B 985 " --> pdb=" O LYS C 374 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1054 through 1056 Processing sheet with id=AC6, first strand: chain 'C' and resid 105 through 114 removed outlier: 9.939A pdb=" N LEU C 109 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 10.501A pdb=" N CYS C 111 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU C 268 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AC8, first strand: chain 'C' and resid 379 through 380 removed outlier: 3.540A pdb=" N GLY C 380 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 384 through 386 Processing sheet with id=AD1, first strand: chain 'C' and resid 580 through 581 removed outlier: 8.052A pdb=" N PHE C 581 " --> pdb=" O ARG C 605 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP C 649 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 622 " --> pdb=" O ILE K 274 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU K 256 " --> pdb=" O ILE K 283 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N HIS K 285 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 215 through 217 Processing sheet with id=AD3, first strand: chain 'D' and resid 226 through 228 removed outlier: 4.355A pdb=" N VAL D 248 " --> pdb=" O ARG D 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 253 through 254 removed outlier: 3.654A pdb=" N ALA D 261 " --> pdb=" O ILE D 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 304 through 305 removed outlier: 3.999A pdb=" N GLY D 310 " --> pdb=" O SER D 305 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 351 through 353 removed outlier: 7.020A pdb=" N VAL D 352 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 422 " --> pdb=" O PHE D 405 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 404 " --> pdb=" O CYS D 381 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 381 " --> pdb=" O SER D 404 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 378 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 370 " --> pdb=" O ALA D 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 397 through 400 removed outlier: 3.543A pdb=" N VAL D 387 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE D 400 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 414 " --> pdb=" O GLY D 358 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN D 412 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 436 through 437 Processing sheet with id=AD9, first strand: chain 'D' and resid 465 through 467 Processing sheet with id=AE1, first strand: chain 'D' and resid 472 through 473 Processing sheet with id=AE2, first strand: chain 'D' and resid 480 through 483 removed outlier: 6.632A pdb=" N GLN D 497 " --> pdb=" O HIS N 367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 567 through 569 Processing sheet with id=AE4, first strand: chain 'D' and resid 602 through 606 removed outlier: 6.385A pdb=" N ILE D 602 " --> pdb=" O LEU D 827 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 827 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ALA D 604 " --> pdb=" O LEU D 825 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 612 through 613 Processing sheet with id=AE6, first strand: chain 'D' and resid 769 through 772 Processing sheet with id=AE7, first strand: chain 'D' and resid 661 through 666 Processing sheet with id=AE8, first strand: chain 'D' and resid 714 through 716 Processing sheet with id=AE9, first strand: chain 'D' and resid 842 through 850 removed outlier: 3.688A pdb=" N VAL D 846 " --> pdb=" O PHE D 857 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE D 857 " --> pdb=" O VAL D 846 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 848 " --> pdb=" O GLN D 855 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 937 through 938 removed outlier: 3.881A pdb=" N VAL D1083 " --> pdb=" O ILE D 938 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 977 through 978 removed outlier: 3.621A pdb=" N VAL N 171 " --> pdb=" O SER D 977 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1073 through 1074 removed outlier: 7.201A pdb=" N PHE D1056 " --> pdb=" O ILE N 95 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 194 through 197 removed outlier: 6.633A pdb=" N LYS E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLY E 169 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ASP E 197 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL E 171 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU E 103 " --> pdb=" O ILE E 245 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N HIS E 247 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS E 105 " --> pdb=" O HIS E 247 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASN E 249 " --> pdb=" O CYS E 105 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N PHE E 107 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N PHE E 246 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ASP E 279 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 248 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 374 " --> pdb=" O ASP E 370 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 219 through 223 removed outlier: 6.240A pdb=" N THR E 221 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG E 208 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 149 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE F 96 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL F 130 " --> pdb=" O ILE F 96 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASP F 98 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LYS F 76 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ASP F 131 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 99 through 101 removed outlier: 3.744A pdb=" N PHE I 111 " --> pdb=" O GLU I 100 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 123 through 129 removed outlier: 6.208A pdb=" N MET I 124 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE I 314 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N MET I 126 " --> pdb=" O VAL I 312 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL I 312 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET I 309 " --> pdb=" O ARG I 304 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AF9, first strand: chain 'K' and resid 121 through 122 removed outlier: 4.166A pdb=" N TYR K 169 " --> pdb=" O VAL K 122 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 131 through 135 removed outlier: 3.774A pdb=" N ILE K 143 " --> pdb=" O HIS K 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE K 134 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE K 141 " --> pdb=" O ILE K 134 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG K 144 " --> pdb=" O GLU K 158 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLU K 158 " --> pdb=" O ARG K 144 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 173 through 174 removed outlier: 6.799A pdb=" N LYS K 173 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ARG K 252 " --> pdb=" O LYS K 173 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER K 249 " --> pdb=" O ASP K 244 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS K 221 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU K 238 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N LEU K 219 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N ILE K 240 " --> pdb=" O VAL K 217 " (cutoff:3.500A) removed outlier: 10.104A pdb=" N VAL K 217 " --> pdb=" O ILE K 240 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 209 through 215 removed outlier: 7.560A pdb=" N GLY L 181 " --> pdb=" O ASP L 232 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP L 232 " --> pdb=" O GLY L 181 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA L 183 " --> pdb=" O THR L 230 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR L 230 " --> pdb=" O ALA L 183 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU L 185 " --> pdb=" O ILE L 228 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 199 through 204 Processing sheet with id=AG5, first strand: chain 'N' and resid 306 through 307 removed outlier: 6.599A pdb=" N ASP N 297 " --> pdb=" O VAL N 285 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL N 285 " --> pdb=" O ASP N 297 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET N 327 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLU N 344 " --> pdb=" O LEU N 331 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 456 through 457 Processing sheet with id=AG7, first strand: chain 'O' and resid 16 through 21 removed outlier: 3.665A pdb=" N VAL O 18 " --> pdb=" O ARG O 31 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG O 31 " --> pdb=" O VAL O 18 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER O 20 " --> pdb=" O TYR O 29 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR O 29 " --> pdb=" O SER O 20 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS O 28 " --> pdb=" O THR O 205 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN O 181 " --> pdb=" O TRP O 204 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 59 through 67 removed outlier: 3.521A pdb=" N ASN O 154 " --> pdb=" O GLY O 59 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN O 150 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA O 65 " --> pdb=" O GLY O 148 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLY O 148 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER O 67 " --> pdb=" O CYS O 146 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N CYS O 146 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG O 153 " --> pdb=" O GLY O 102 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY O 102 " --> pdb=" O ARG O 153 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 59 through 67 removed outlier: 3.521A pdb=" N ASN O 154 " --> pdb=" O GLY O 59 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN O 150 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA O 65 " --> pdb=" O GLY O 148 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLY O 148 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER O 67 " --> pdb=" O CYS O 146 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N CYS O 146 " --> pdb=" O SER O 67 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 145 " --> pdb=" O VAL O 110 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL O 110 " --> pdb=" O LEU O 145 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 96 through 98 Processing sheet with id=AH2, first strand: chain 'O' and resid 115 through 117 removed outlier: 7.219A pdb=" N VAL O 116 " --> pdb=" O ILE O 136 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 66 through 70 removed outlier: 3.734A pdb=" N THR Q 66 " --> pdb=" O TYR Q 131 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Q' and resid 75 through 77 Processing sheet with id=AH5, first strand: chain 'Q' and resid 83 through 84 Processing sheet with id=AH6, first strand: chain 'R' and resid 99 through 100 Processing sheet with id=AH7, first strand: chain 'S' and resid 201 through 204 removed outlier: 6.038A pdb=" N CYS S 202 " --> pdb=" O TYR S 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'S' and resid 403 through 404 removed outlier: 3.599A pdb=" N VAL S 404 " --> pdb=" O PHE S 451 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 245 through 246 removed outlier: 3.824A pdb=" N MET J 245 " --> pdb=" O ILE J 269 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 419 through 423 removed outlier: 5.965A pdb=" N SER J 349 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N MET J 422 " --> pdb=" O SER J 349 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE J 351 " --> pdb=" O MET J 422 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE J 441 " --> pdb=" O VAL J 350 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY J 352 " --> pdb=" O ILE J 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL J 443 " --> pdb=" O GLY J 352 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA J 442 " --> pdb=" O ILE J 481 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 386 through 388 removed outlier: 4.401A pdb=" N HIS J 388 " --> pdb=" O ASN J 391 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 515 through 521 removed outlier: 3.616A pdb=" N HIS J 515 " --> pdb=" O ASN J 531 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU J 529 " --> pdb=" O LEU J 517 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE J 519 " --> pdb=" O THR J 527 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR J 527 " --> pdb=" O PHE J 519 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 648 through 651 removed outlier: 3.863A pdb=" N THR J 622 " --> pdb=" O VAL J 648 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 730 through 731 removed outlier: 3.679A pdb=" N GLN J 731 " --> pdb=" O GLU J 738 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU J 738 " --> pdb=" O GLN J 731 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 1937 hydrogen bonds defined for protein. 5340 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: 27.18 Time building geometry restraints manager: 12.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10180 1.32 - 1.45: 15810 1.45 - 1.58: 33821 1.58 - 1.70: 1 1.70 - 1.83: 471 Bond restraints: 60283 Sorted by residual: bond pdb=" CA SER D 416 " pdb=" C SER D 416 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.88e+01 bond pdb=" CA LYS C 49 " pdb=" C LYS C 49 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.27e-02 6.20e+03 1.26e+01 bond pdb=" C LYS S 318 " pdb=" O LYS S 318 " ideal model delta sigma weight residual 1.249 1.219 0.030 8.50e-03 1.38e+04 1.25e+01 bond pdb=" CA PRO L 202 " pdb=" C PRO L 202 " ideal model delta sigma weight residual 1.520 1.470 0.049 1.42e-02 4.96e+03 1.20e+01 bond pdb=" CA ALA S 307 " pdb=" C ALA S 307 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.14e+01 ... (remaining 60278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 80663 2.79 - 5.58: 866 5.58 - 8.37: 102 8.37 - 11.16: 25 11.16 - 13.95: 6 Bond angle restraints: 81662 Sorted by residual: angle pdb=" N LEU D 333 " pdb=" CA LEU D 333 " pdb=" C LEU D 333 " ideal model delta sigma weight residual 112.87 99.79 13.08 1.20e+00 6.94e-01 1.19e+02 angle pdb=" N GLN D 332 " pdb=" CA GLN D 332 " pdb=" C GLN D 332 " ideal model delta sigma weight residual 112.90 98.95 13.95 1.31e+00 5.83e-01 1.13e+02 angle pdb=" N SER B 185 " pdb=" CA SER B 185 " pdb=" C SER B 185 " ideal model delta sigma weight residual 112.72 102.74 9.98 1.14e+00 7.69e-01 7.66e+01 angle pdb=" C LEU D1130 " pdb=" N PRO D1131 " pdb=" CA PRO D1131 " ideal model delta sigma weight residual 119.19 110.56 8.63 1.06e+00 8.90e-01 6.62e+01 angle pdb=" N TYR H 334 " pdb=" CA TYR H 334 " pdb=" C TYR H 334 " ideal model delta sigma weight residual 110.52 98.64 11.88 1.48e+00 4.57e-01 6.45e+01 ... (remaining 81657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 30864 18.01 - 36.02: 4154 36.02 - 54.03: 1094 54.03 - 72.04: 176 72.04 - 90.05: 86 Dihedral angle restraints: 36374 sinusoidal: 14613 harmonic: 21761 Sorted by residual: dihedral pdb=" CB CYS R 104 " pdb=" SG CYS R 104 " pdb=" SG CYS R 107 " pdb=" CB CYS R 107 " ideal model delta sinusoidal sigma weight residual -86.00 -154.14 68.14 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CA ASP L 224 " pdb=" C ASP L 224 " pdb=" N TYR L 225 " pdb=" CA TYR L 225 " ideal model delta harmonic sigma weight residual -180.00 -150.40 -29.60 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP H 430 " pdb=" C ASP H 430 " pdb=" N TYR H 431 " pdb=" CA TYR H 431 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 36371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 7344 0.057 - 0.114: 1398 0.114 - 0.171: 177 0.171 - 0.227: 13 0.227 - 0.284: 4 Chirality restraints: 8936 Sorted by residual: chirality pdb=" CA ALA S 314 " pdb=" N ALA S 314 " pdb=" C ALA S 314 " pdb=" CB ALA S 314 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA VAL H 336 " pdb=" N VAL H 336 " pdb=" C VAL H 336 " pdb=" CB VAL H 336 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE B 178 " pdb=" CA ILE B 178 " pdb=" CG1 ILE B 178 " pdb=" CG2 ILE B 178 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 8933 not shown) Planarity restraints: 10667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN H 468 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.81e+01 pdb=" N PRO H 469 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO H 469 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 469 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 500 " 0.065 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO J 501 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO J 501 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 501 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 122 " 0.062 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO C 123 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.051 5.00e-02 4.00e+02 ... (remaining 10664 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1994 2.70 - 3.25: 58104 3.25 - 3.80: 90947 3.80 - 4.35: 118568 4.35 - 4.90: 196473 Nonbonded interactions: 466086 Sorted by model distance: nonbonded pdb=" NE2 HIS L 81 " pdb="FE FE L 301 " model vdw 2.149 2.340 nonbonded pdb=" O GLY D 426 " pdb=" OG1 THR D 427 " model vdw 2.150 3.040 nonbonded pdb=" OG SER E 470 " pdb=" OE1 GLU G 231 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG R 88 " pdb=" O PRO R 157 " model vdw 2.201 3.120 nonbonded pdb=" O THR B1023 " pdb=" NH2 ARG C 412 " model vdw 2.208 3.120 ... (remaining 466081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 231) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'R' } 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=0.00 max=1.00 mean=0.97 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: 7.900 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: 0.070 Extract box with map and model: 1.670 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 110.900 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 60283 Z= 0.226 Angle : 0.721 13.949 81662 Z= 0.405 Chirality : 0.045 0.284 8936 Planarity : 0.005 0.107 10667 Dihedral : 17.676 90.047 22342 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.94 % Favored : 88.16 % Rotamer: Outliers : 1.48 % Allowed : 25.88 % Favored : 72.64 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 7454 helix: -0.17 (0.11), residues: 2329 sheet: -1.30 (0.18), residues: 898 loop : -2.43 (0.09), residues: 4227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP S 529 HIS 0.013 0.001 HIS P 129 PHE 0.057 0.001 PHE D1170 TYR 0.031 0.001 TYR D1251 ARG 0.011 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 722 time to evaluate : 5.085 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: B 948 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8782 (mt) REVERT: D 1122 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6610 (mmt180) REVERT: H 78 MET cc_start: 0.6389 (mmt) cc_final: 0.6171 (mmt) REVERT: H 338 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7962 (mtm-85) REVERT: H 724 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: H 752 GLU cc_start: 0.1313 (OUTLIER) cc_final: -0.0547 (mt-10) REVERT: I 350 ASN cc_start: 0.5894 (p0) cc_final: 0.5514 (p0) REVERT: I 445 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: N 546 GLU cc_start: 0.6497 (pp20) cc_final: 0.6251 (tt0) REVERT: P 124 ARG cc_start: 0.7532 (tpt170) cc_final: 0.7159 (tpt-90) REVERT: R 142 MET cc_start: 0.3903 (mmm) cc_final: 0.2541 (mmm) REVERT: S 340 MET cc_start: 0.5144 (mmm) cc_final: 0.3658 (mmm) REVERT: S 415 MET cc_start: 0.3945 (mmt) cc_final: 0.3731 (tpt) REVERT: S 510 LYS cc_start: 0.8572 (tptt) cc_final: 0.8297 (mmmm) REVERT: J 713 MET cc_start: 0.4597 (tmm) cc_final: 0.3835 (tpp) outliers start: 91 outliers final: 36 residues processed: 795 average time/residue: 0.5908 time to fit residues: 783.8512 Evaluate side-chains 730 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 688 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 369 PRO Chi-restraints excluded: chain D residue 1120 LYS Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1127 THR Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 724 GLU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain H residue 837 SER Chi-restraints excluded: chain I residue 362 ARG Chi-restraints excluded: chain I residue 445 GLN Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 177 GLN Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 82 ASP Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain S residue 209 HIS Chi-restraints excluded: chain S residue 305 LYS Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 506 LEU Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 693 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 625 optimal weight: 5.9990 chunk 561 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 378 optimal weight: 0.0770 chunk 300 optimal weight: 0.9980 chunk 580 optimal weight: 2.9990 chunk 224 optimal weight: 0.0470 chunk 353 optimal weight: 2.9990 chunk 432 optimal weight: 8.9990 chunk 672 optimal weight: 7.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 154 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN B 229 GLN B 483 ASN B 540 ASN B 805 HIS B 971 GLN B 983 GLN C 44 HIS ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN ** D 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS H 254 GLN H 285 ASN ** H 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN I 485 GLN ** K 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN L 177 GLN L 244 ASN M 88 GLN ** M 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 233 ASN P 122 ASN ** P 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 GLN ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.177933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127278 restraints weight = 95607.787| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.70 r_work: 0.3423 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 60283 Z= 0.202 Angle : 0.637 11.407 81662 Z= 0.333 Chirality : 0.045 0.221 8936 Planarity : 0.005 0.095 10667 Dihedral : 6.430 83.637 8309 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.96 % Favored : 88.38 % Rotamer: Outliers : 3.93 % Allowed : 23.95 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 7454 helix: 0.08 (0.11), residues: 2424 sheet: -1.32 (0.17), residues: 926 loop : -2.39 (0.09), residues: 4104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 761 HIS 0.009 0.001 HIS P 129 PHE 0.065 0.001 PHE D1170 TYR 0.024 0.001 TYR B 679 ARG 0.007 0.000 ARG D 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 242 poor density : 748 time to evaluate : 5.022 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: A 114 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6475 (ttt180) REVERT: B 71 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.6935 (m-10) REVERT: B 171 ARG cc_start: 0.4879 (tpp80) cc_final: 0.4455 (tpp80) REVERT: B 589 TYR cc_start: 0.8005 (t80) cc_final: 0.7307 (t80) REVERT: B 591 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7624 (m-40) REVERT: B 948 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8889 (mt) REVERT: B 961 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6277 (ttt-90) REVERT: B 1014 LYS cc_start: 0.7701 (ptmt) cc_final: 0.6676 (ttmt) REVERT: B 1045 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: D 231 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7120 (mm-40) REVERT: D 1122 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6783 (mmt180) REVERT: H 78 MET cc_start: 0.6556 (mmt) cc_final: 0.6240 (mmt) REVERT: H 338 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7853 (mtm-85) REVERT: H 724 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6186 (mm-30) REVERT: H 752 GLU cc_start: 0.0875 (OUTLIER) cc_final: -0.1137 (mt-10) REVERT: H 802 ILE cc_start: 0.3034 (OUTLIER) cc_final: 0.2644 (tp) REVERT: H 824 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6337 (tp) REVERT: I 220 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: I 232 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7951 (tm-30) REVERT: I 350 ASN cc_start: 0.6626 (p0) cc_final: 0.6115 (p0) REVERT: K 291 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7799 (t0) REVERT: L 131 TRP cc_start: 0.8290 (t60) cc_final: 0.8007 (t60) REVERT: L 188 LYS cc_start: 0.7485 (tptp) cc_final: 0.7122 (tptp) REVERT: L 277 ARG cc_start: 0.8344 (mtt180) cc_final: 0.8119 (mtp180) REVERT: N 235 TRP cc_start: 0.9303 (t60) cc_final: 0.9060 (t60) REVERT: N 377 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8311 (tt) REVERT: O 154 ASN cc_start: 0.7868 (m110) cc_final: 0.7480 (m110) REVERT: O 155 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.6955 (ttp80) REVERT: O 197 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8118 (mp0) REVERT: P 86 GLU cc_start: 0.8370 (pm20) cc_final: 0.8090 (pm20) REVERT: S 340 MET cc_start: 0.4371 (mmm) cc_final: 0.2941 (mmm) REVERT: S 415 MET cc_start: 0.4187 (mmt) cc_final: 0.3902 (tpt) outliers start: 242 outliers final: 98 residues processed: 932 average time/residue: 0.5761 time to fit residues: 904.2894 Evaluate side-chains 795 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 681 time to evaluate : 5.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 591 ASN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1271 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 724 GLU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 824 ILE Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain H residue 837 SER Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 270 MET Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 86 HIS Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 463 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain O residue 155 ARG Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 122 ASN Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 506 LEU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 691 LEU Chi-restraints excluded: chain J residue 693 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 666 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 498 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 271 optimal weight: 40.0000 chunk 169 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 449 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 585 optimal weight: 0.9990 chunk 644 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN B 483 ASN B 536 HIS B 805 HIS C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS ** H 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 ASN ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN K 132 HIS K 229 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 ASN O 231 HIS P 122 ASN ** P 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN J 693 ASN J 727 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.175073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124488 restraints weight = 96003.385| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.91 r_work: 0.3353 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 60283 Z= 0.312 Angle : 0.655 9.864 81662 Z= 0.343 Chirality : 0.046 0.226 8936 Planarity : 0.005 0.095 10667 Dihedral : 6.133 90.608 8266 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.77 % Favored : 87.61 % Rotamer: Outliers : 4.20 % Allowed : 24.03 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 7454 helix: 0.01 (0.11), residues: 2453 sheet: -1.40 (0.17), residues: 935 loop : -2.43 (0.09), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 761 HIS 0.015 0.001 HIS J 727 PHE 0.064 0.002 PHE D1170 TYR 0.031 0.002 TYR B 71 ARG 0.008 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 687 time to evaluate : 5.158 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: A 69 LYS cc_start: 0.7480 (mmtm) cc_final: 0.7070 (tppt) REVERT: A 114 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6491 (ttt180) REVERT: A 220 ARG cc_start: 0.6337 (OUTLIER) cc_final: 0.6060 (ttp-170) REVERT: A 224 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6974 (m-30) REVERT: B 71 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: B 171 ARG cc_start: 0.4926 (tpp80) cc_final: 0.4475 (tpp80) REVERT: B 178 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7442 (tp) REVERT: B 941 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 948 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8988 (mt) REVERT: B 961 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6513 (ttt-90) REVERT: B 1014 LYS cc_start: 0.7816 (ptmt) cc_final: 0.6795 (ttmt) REVERT: B 1045 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: B 1052 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7402 (mt-10) REVERT: C 239 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: C 588 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (mp) REVERT: C 617 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: D 231 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7185 (mm-40) REVERT: D 1122 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6753 (mmt90) REVERT: E 472 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.7883 (p90) REVERT: G 191 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.4448 (m-10) REVERT: G 314 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7182 (mm-30) REVERT: G 420 LEU cc_start: 0.8539 (mp) cc_final: 0.8317 (mp) REVERT: H 78 MET cc_start: 0.6532 (mmt) cc_final: 0.6180 (mmt) REVERT: H 432 MET cc_start: 0.7582 (tpp) cc_final: 0.7378 (tpp) REVERT: H 510 TYR cc_start: 0.6124 (p90) cc_final: 0.5543 (p90) REVERT: H 724 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: H 752 GLU cc_start: 0.0881 (OUTLIER) cc_final: -0.1338 (mt-10) REVERT: H 824 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6446 (tp) REVERT: H 829 HIS cc_start: 0.5546 (OUTLIER) cc_final: 0.3620 (t70) REVERT: I 101 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: I 220 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: I 228 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7159 (t-90) REVERT: I 350 ASN cc_start: 0.6779 (p0) cc_final: 0.6150 (p0) REVERT: K 151 ASN cc_start: 0.8966 (t0) cc_final: 0.8736 (t0) REVERT: K 291 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7698 (t0) REVERT: L 131 TRP cc_start: 0.8349 (t60) cc_final: 0.7793 (t60) REVERT: L 188 LYS cc_start: 0.7217 (tptp) cc_final: 0.6663 (tptp) REVERT: N 345 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (mt) REVERT: N 421 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.5009 (tp) REVERT: N 449 HIS cc_start: 0.7441 (m90) cc_final: 0.7060 (m90) REVERT: O 70 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.5846 (mp) REVERT: O 154 ASN cc_start: 0.7835 (m110) cc_final: 0.7338 (m110) REVERT: O 155 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.6882 (ttp80) REVERT: P 81 MET cc_start: 0.7415 (mmt) cc_final: 0.7161 (mtt) REVERT: P 86 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: P 91 MET cc_start: 0.9071 (ttt) cc_final: 0.8795 (ttt) REVERT: P 96 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7614 (p0) REVERT: P 97 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8636 (ttt180) REVERT: S 358 MET cc_start: -0.0285 (mpp) cc_final: -0.0548 (mpp) REVERT: S 428 ARG cc_start: 0.2873 (OUTLIER) cc_final: 0.2606 (tpm170) REVERT: S 478 MET cc_start: 0.2783 (mpp) cc_final: 0.1852 (mpp) REVERT: S 481 PHE cc_start: -0.0611 (OUTLIER) cc_final: -0.2392 (m-80) REVERT: S 498 ARG cc_start: 0.4303 (tpt170) cc_final: 0.4024 (ttt180) REVERT: S 510 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7537 (tptp) REVERT: J 377 THR cc_start: 0.1617 (OUTLIER) cc_final: 0.1128 (t) REVERT: J 401 ASP cc_start: 0.3270 (OUTLIER) cc_final: 0.1732 (m-30) REVERT: J 688 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: J 713 MET cc_start: 0.5170 (tmm) cc_final: 0.4272 (tpp) outliers start: 259 outliers final: 141 residues processed: 883 average time/residue: 0.5623 time to fit residues: 840.6864 Evaluate side-chains 827 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 652 time to evaluate : 5.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 466 TYR Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 724 GLU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 824 ILE Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 179 MET Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 495 GLU Chi-restraints excluded: chain N residue 506 LEU Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 155 ARG Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 LYS Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 381 LEU Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 428 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 506 LEU Chi-restraints excluded: chain S residue 529 TRP Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 720 optimal weight: 7.9990 chunk 594 optimal weight: 5.9990 chunk 652 optimal weight: 4.9990 chunk 463 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 412 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 550 optimal weight: 5.9990 chunk 348 optimal weight: 0.9980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN B 805 HIS ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS ** H 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN I 445 GLN K 229 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN ** M 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 503 GLN J 399 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.173473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122279 restraints weight = 96126.947| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.78 r_work: 0.3347 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 60283 Z= 0.364 Angle : 0.677 14.250 81662 Z= 0.354 Chirality : 0.047 0.234 8936 Planarity : 0.005 0.095 10667 Dihedral : 6.198 100.885 8256 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 12.25 % Favored : 87.16 % Rotamer: Outliers : 5.26 % Allowed : 23.85 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 7454 helix: -0.08 (0.11), residues: 2442 sheet: -1.48 (0.17), residues: 939 loop : -2.50 (0.09), residues: 4073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 763 HIS 0.012 0.001 HIS D 449 PHE 0.064 0.002 PHE D1170 TYR 0.028 0.002 TYR B 71 ARG 0.008 0.000 ARG I 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 324 poor density : 682 time to evaluate : 5.291 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: A 224 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: B 55 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: B 71 TYR cc_start: 0.8012 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 169 TRP cc_start: 0.4617 (OUTLIER) cc_final: 0.4111 (p90) REVERT: B 171 ARG cc_start: 0.4968 (tpp80) cc_final: 0.4512 (tpp80) REVERT: B 178 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7510 (tp) REVERT: B 570 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: B 889 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.6196 (mm-30) REVERT: B 941 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 948 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8977 (mt) REVERT: B 961 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6649 (ttt-90) REVERT: B 1014 LYS cc_start: 0.7878 (ptmt) cc_final: 0.6842 (ttmt) REVERT: B 1045 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7813 (pm20) REVERT: B 1052 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7558 (mt-10) REVERT: C 239 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7161 (mtm-85) REVERT: C 573 TYR cc_start: 0.1407 (OUTLIER) cc_final: 0.0393 (m-10) REVERT: C 588 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8844 (mp) REVERT: C 602 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8941 (pp) REVERT: D 231 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7226 (mm-40) REVERT: D 1122 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6935 (mmt180) REVERT: D 1210 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8244 (tpt170) REVERT: E 472 TRP cc_start: 0.8649 (OUTLIER) cc_final: 0.7945 (p90) REVERT: G 191 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.4407 (m-10) REVERT: G 351 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8412 (tp) REVERT: G 420 LEU cc_start: 0.8545 (mp) cc_final: 0.8334 (mp) REVERT: H 434 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7233 (ptt90) REVERT: H 510 TYR cc_start: 0.6230 (p90) cc_final: 0.5696 (p90) REVERT: H 726 ASP cc_start: 0.5783 (m-30) cc_final: 0.5192 (m-30) REVERT: H 829 HIS cc_start: 0.5174 (OUTLIER) cc_final: 0.3527 (t70) REVERT: I 101 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: I 165 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8828 (pptt) REVERT: I 220 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6785 (tp30) REVERT: I 228 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7130 (t-90) REVERT: I 350 ASN cc_start: 0.7059 (p0) cc_final: 0.6424 (p0) REVERT: I 445 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7998 (tp40) REVERT: K 151 ASN cc_start: 0.8880 (t0) cc_final: 0.8550 (t0) REVERT: K 303 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7869 (ptp90) REVERT: L 79 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: L 131 TRP cc_start: 0.8189 (t60) cc_final: 0.7798 (t60) REVERT: L 221 LEU cc_start: 0.8313 (pp) cc_final: 0.8056 (pp) REVERT: L 235 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: N 345 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8194 (mt) REVERT: N 377 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8341 (tt) REVERT: N 397 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: N 449 HIS cc_start: 0.7499 (m90) cc_final: 0.7090 (m90) REVERT: N 546 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6162 (pp20) REVERT: O 70 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.5919 (mp) REVERT: O 154 ASN cc_start: 0.7825 (m110) cc_final: 0.7287 (m110) REVERT: P 86 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: P 91 MET cc_start: 0.9059 (ttt) cc_final: 0.8852 (ttt) REVERT: P 97 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (ttt180) REVERT: P 122 ASN cc_start: 0.8491 (m-40) cc_final: 0.8203 (p0) REVERT: Q 122 TRP cc_start: 0.7074 (m100) cc_final: 0.6762 (m100) REVERT: R 110 MET cc_start: 0.5134 (tpp) cc_final: 0.4595 (mtp) REVERT: S 303 GLN cc_start: 0.3637 (OUTLIER) cc_final: 0.3012 (mp10) REVERT: S 340 MET cc_start: 0.4379 (mmm) cc_final: 0.3096 (mmm) REVERT: S 498 ARG cc_start: 0.4363 (tpt170) cc_final: 0.4054 (ttt180) REVERT: J 377 THR cc_start: 0.1641 (OUTLIER) cc_final: 0.1111 (t) REVERT: J 379 MET cc_start: 0.3638 (tpt) cc_final: 0.3394 (tpp) REVERT: J 401 ASP cc_start: 0.3312 (OUTLIER) cc_final: 0.1727 (m-30) REVERT: J 469 PHE cc_start: -0.0917 (m-80) cc_final: -0.1363 (m-80) REVERT: J 713 MET cc_start: 0.5287 (tmm) cc_final: 0.4457 (tpp) outliers start: 324 outliers final: 184 residues processed: 937 average time/residue: 0.5513 time to fit residues: 875.6973 Evaluate side-chains 865 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 642 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 889 GLU Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1136 VAL Chi-restraints excluded: chain D residue 1189 ILE Chi-restraints excluded: chain D residue 1210 ARG Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 466 TYR Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain I residue 445 GLN Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 489 LEU Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 415 VAL Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 495 GLU Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 534 ILE Chi-restraints excluded: chain N residue 546 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 374 ASP Chi-restraints excluded: chain S residue 381 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 529 TRP Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 703 optimal weight: 0.0060 chunk 233 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 695 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 484 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 465 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN B 540 ASN C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS ** H 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN K 229 ASN L 92 ASN L 219 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.176842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126715 restraints weight = 95907.903| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.91 r_work: 0.3387 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 60283 Z= 0.183 Angle : 0.609 11.138 81662 Z= 0.317 Chirality : 0.044 0.232 8936 Planarity : 0.004 0.096 10667 Dihedral : 5.854 100.863 8247 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.86 % Favored : 88.58 % Rotamer: Outliers : 4.46 % Allowed : 24.83 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 7454 helix: 0.16 (0.11), residues: 2434 sheet: -1.37 (0.18), residues: 918 loop : -2.41 (0.09), residues: 4102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 761 HIS 0.007 0.001 HIS P 129 PHE 0.061 0.001 PHE D1170 TYR 0.024 0.001 TYR B 71 ARG 0.006 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 721 time to evaluate : 5.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6447 (ttt180) REVERT: B 55 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: B 71 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: B 154 TRP cc_start: 0.7133 (m100) cc_final: 0.6784 (m100) REVERT: B 169 TRP cc_start: 0.4593 (OUTLIER) cc_final: 0.4173 (p90) REVERT: B 171 ARG cc_start: 0.4932 (tpp80) cc_final: 0.4455 (tpp80) REVERT: B 178 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7428 (tp) REVERT: B 257 GLU cc_start: 0.6829 (tm-30) cc_final: 0.5736 (tm-30) REVERT: B 948 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8907 (mt) REVERT: B 961 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6504 (ttt-90) REVERT: B 988 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7897 (mtt) REVERT: B 1014 LYS cc_start: 0.7852 (ptmt) cc_final: 0.6837 (ttmt) REVERT: B 1045 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: B 1052 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 239 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7208 (mtm-85) REVERT: C 533 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: C 573 TYR cc_start: 0.1418 (OUTLIER) cc_final: 0.0430 (m-10) REVERT: D 1122 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6874 (mmt90) REVERT: E 472 TRP cc_start: 0.8460 (OUTLIER) cc_final: 0.7764 (p90) REVERT: G 191 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.4549 (m-10) REVERT: G 351 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8397 (tp) REVERT: G 420 LEU cc_start: 0.8563 (mp) cc_final: 0.8357 (mp) REVERT: H 121 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.5990 (mp0) REVERT: H 434 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7128 (ptt90) REVERT: H 461 VAL cc_start: 0.5287 (OUTLIER) cc_final: 0.4973 (t) REVERT: H 789 ILE cc_start: 0.7392 (tt) cc_final: 0.7137 (pt) REVERT: H 829 HIS cc_start: 0.5103 (OUTLIER) cc_final: 0.3508 (t70) REVERT: I 101 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: I 165 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (pptt) REVERT: I 220 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6823 (tp30) REVERT: I 228 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7109 (t-90) REVERT: K 151 ASN cc_start: 0.8899 (t0) cc_final: 0.8569 (t0) REVERT: L 131 TRP cc_start: 0.8020 (t60) cc_final: 0.7696 (t60) REVERT: L 219 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6244 (m-40) REVERT: L 235 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: N 345 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8135 (mt) REVERT: N 377 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (tt) REVERT: N 397 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: N 421 LEU cc_start: 0.5176 (OUTLIER) cc_final: 0.4932 (tp) REVERT: N 449 HIS cc_start: 0.7431 (m90) cc_final: 0.6981 (m90) REVERT: O 70 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.5890 (mp) REVERT: O 89 MET cc_start: 0.7131 (mmm) cc_final: 0.6904 (mmm) REVERT: O 154 ASN cc_start: 0.7800 (m110) cc_final: 0.7343 (m-40) REVERT: O 155 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.6936 (ttp80) REVERT: O 197 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7982 (mp0) REVERT: P 86 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: P 91 MET cc_start: 0.8999 (ttt) cc_final: 0.8774 (ttt) REVERT: P 97 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8576 (ttt180) REVERT: P 122 ASN cc_start: 0.8440 (m-40) cc_final: 0.8196 (p0) REVERT: Q 122 TRP cc_start: 0.7118 (m100) cc_final: 0.6815 (m100) REVERT: R 110 MET cc_start: 0.5076 (tpp) cc_final: 0.4439 (mtt) REVERT: S 265 MET cc_start: 0.2248 (OUTLIER) cc_final: 0.1690 (pmm) REVERT: S 303 GLN cc_start: 0.3508 (OUTLIER) cc_final: 0.3004 (mp10) REVERT: S 340 MET cc_start: 0.4421 (mmm) cc_final: 0.3391 (mmm) REVERT: S 478 MET cc_start: 0.2450 (mpp) cc_final: 0.1224 (mpp) REVERT: S 481 PHE cc_start: -0.0816 (OUTLIER) cc_final: -0.2249 (m-80) REVERT: S 498 ARG cc_start: 0.4563 (tpt170) cc_final: 0.4350 (ttt180) REVERT: S 526 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6067 (mt) REVERT: J 245 MET cc_start: 0.5027 (ttm) cc_final: 0.4632 (ttp) REVERT: J 469 PHE cc_start: -0.0674 (m-80) cc_final: -0.1014 (m-80) REVERT: J 713 MET cc_start: 0.5411 (tmm) cc_final: 0.5114 (tmm) REVERT: J 752 TYR cc_start: 0.5966 (m-80) cc_final: 0.5684 (m-80) outliers start: 275 outliers final: 159 residues processed: 935 average time/residue: 0.5598 time to fit residues: 885.3836 Evaluate side-chains 861 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 665 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 489 LEU Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 155 ARG Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 265 MET Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 381 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 496 LEU Chi-restraints excluded: chain S residue 526 ILE Chi-restraints excluded: chain J residue 259 ILE Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 347 SER Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 158 optimal weight: 10.0000 chunk 566 optimal weight: 8.9990 chunk 698 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 506 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 464 optimal weight: 3.9990 chunk 688 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 342 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN B 540 ASN B 591 ASN C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 87 HIS H 140 HIS ** H 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN K 229 ASN ** L 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN J 427 ASN ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.125381 restraints weight = 96006.235| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.00 r_work: 0.3356 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 60283 Z= 0.281 Angle : 0.637 13.394 81662 Z= 0.330 Chirality : 0.045 0.240 8936 Planarity : 0.005 0.096 10667 Dihedral : 5.887 103.198 8247 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.58 % Favored : 87.85 % Rotamer: Outliers : 4.77 % Allowed : 24.92 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.10), residues: 7454 helix: 0.11 (0.11), residues: 2447 sheet: -1.44 (0.17), residues: 940 loop : -2.43 (0.09), residues: 4067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 763 HIS 0.008 0.001 HIS D 449 PHE 0.060 0.001 PHE D1170 TYR 0.024 0.001 TYR B 71 ARG 0.008 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 674 time to evaluate : 5.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6485 (ttt180) REVERT: B 55 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: B 71 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: B 154 TRP cc_start: 0.7168 (m100) cc_final: 0.6876 (m100) REVERT: B 169 TRP cc_start: 0.4737 (OUTLIER) cc_final: 0.4260 (p90) REVERT: B 171 ARG cc_start: 0.4890 (tpp80) cc_final: 0.4438 (tpp80) REVERT: B 178 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7491 (tp) REVERT: B 503 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8511 (mt0) REVERT: B 589 TYR cc_start: 0.7896 (t80) cc_final: 0.7691 (t80) REVERT: B 941 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 948 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8978 (mt) REVERT: B 961 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6582 (ttt-90) REVERT: B 988 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: B 1014 LYS cc_start: 0.7910 (ptmt) cc_final: 0.6902 (ttmt) REVERT: B 1045 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7875 (pm20) REVERT: B 1052 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7498 (mt-10) REVERT: C 239 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7192 (mtm-85) REVERT: C 514 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: C 533 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8395 (pm20) REVERT: C 573 TYR cc_start: 0.1430 (OUTLIER) cc_final: 0.0357 (m-10) REVERT: D 1122 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6982 (mmt180) REVERT: D 1168 TRP cc_start: 0.6142 (OUTLIER) cc_final: 0.5202 (m100) REVERT: D 1210 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (tpt170) REVERT: D 1237 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7816 (tpp80) REVERT: D 1271 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: E 472 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7840 (p90) REVERT: G 191 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.4625 (m-10) REVERT: G 420 LEU cc_start: 0.8564 (mp) cc_final: 0.8354 (mp) REVERT: H 434 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7094 (ptt90) REVERT: H 461 VAL cc_start: 0.4977 (OUTLIER) cc_final: 0.4735 (t) REVERT: H 789 ILE cc_start: 0.7423 (tt) cc_final: 0.7108 (pt) REVERT: H 829 HIS cc_start: 0.5196 (OUTLIER) cc_final: 0.3541 (t70) REVERT: I 101 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: I 165 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8787 (pptt) REVERT: I 220 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6760 (tp30) REVERT: I 228 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7171 (t-90) REVERT: K 151 ASN cc_start: 0.8883 (t0) cc_final: 0.8560 (t0) REVERT: K 303 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7902 (ptp90) REVERT: L 131 TRP cc_start: 0.8371 (t60) cc_final: 0.7565 (t60) REVERT: L 235 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: N 345 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8175 (mt) REVERT: N 377 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8357 (tt) REVERT: N 397 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7773 (pp20) REVERT: N 421 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4994 (tp) REVERT: N 449 HIS cc_start: 0.7484 (m90) cc_final: 0.7071 (m90) REVERT: O 47 ILE cc_start: 0.8524 (mt) cc_final: 0.8284 (mt) REVERT: O 70 ILE cc_start: 0.6258 (OUTLIER) cc_final: 0.5883 (mp) REVERT: O 154 ASN cc_start: 0.7867 (m110) cc_final: 0.7328 (m110) REVERT: P 86 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: P 97 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8655 (ttt180) REVERT: P 122 ASN cc_start: 0.8467 (m-40) cc_final: 0.8112 (p0) REVERT: R 110 MET cc_start: 0.5156 (tpp) cc_final: 0.4586 (mtt) REVERT: S 303 GLN cc_start: 0.3577 (OUTLIER) cc_final: 0.2917 (mp10) REVERT: S 304 MET cc_start: 0.4672 (tpp) cc_final: 0.3634 (tpp) REVERT: S 340 MET cc_start: 0.4485 (mmm) cc_final: 0.3419 (mmm) REVERT: S 498 ARG cc_start: 0.4635 (tpt170) cc_final: 0.4250 (ttt180) REVERT: S 514 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6345 (tm-30) REVERT: J 469 PHE cc_start: -0.0638 (m-80) cc_final: -0.0970 (m-80) REVERT: J 650 MET cc_start: 0.1550 (tpp) cc_final: 0.0986 (mtt) REVERT: J 713 MET cc_start: 0.5371 (tmm) cc_final: 0.5110 (tmm) outliers start: 294 outliers final: 190 residues processed: 906 average time/residue: 0.5736 time to fit residues: 882.1672 Evaluate side-chains 882 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 653 time to evaluate : 5.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 953 GLN Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1168 TRP Chi-restraints excluded: chain D residue 1210 ARG Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1237 ARG Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1271 GLU Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 369 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 783 VAL Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 189 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 534 ILE Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 34 LEU Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 374 ASP Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 496 LEU Chi-restraints excluded: chain S residue 514 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 254 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 chunk 473 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 388 optimal weight: 0.0050 chunk 290 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 702 optimal weight: 7.9990 chunk 530 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 overall best weight: 3.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN B 953 GLN C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS H 394 ASN ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN J 427 ASN ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.172602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122905 restraints weight = 95922.200| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.81 r_work: 0.3335 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 60283 Z= 0.412 Angle : 0.700 11.839 81662 Z= 0.365 Chirality : 0.048 0.247 8936 Planarity : 0.005 0.097 10667 Dihedral : 6.074 112.262 8244 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.67 % Favored : 86.75 % Rotamer: Outliers : 5.09 % Allowed : 24.70 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.10), residues: 7454 helix: -0.07 (0.11), residues: 2442 sheet: -1.57 (0.18), residues: 919 loop : -2.50 (0.09), residues: 4093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP L 131 HIS 0.013 0.001 HIS D 449 PHE 0.066 0.002 PHE D1170 TYR 0.024 0.002 TYR B 679 ARG 0.009 0.001 ARG I 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 314 poor density : 674 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: B 71 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: B 169 TRP cc_start: 0.4652 (OUTLIER) cc_final: 0.4181 (p90) REVERT: B 171 ARG cc_start: 0.4878 (tpp80) cc_final: 0.4386 (tpp80) REVERT: B 178 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7553 (tp) REVERT: B 590 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 889 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: B 941 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8305 (tp) REVERT: B 961 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6735 (ttt-90) REVERT: B 988 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7925 (mtt) REVERT: B 1010 SER cc_start: 0.8140 (m) cc_final: 0.7611 (p) REVERT: B 1045 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: B 1052 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7566 (mt-10) REVERT: C 225 GLU cc_start: 0.4782 (mm-30) cc_final: 0.4582 (mm-30) REVERT: C 239 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: C 514 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: C 533 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: C 573 TYR cc_start: 0.1137 (OUTLIER) cc_final: 0.0032 (m-10) REVERT: D 163 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9039 (mp) REVERT: D 201 TYR cc_start: 0.8083 (t80) cc_final: 0.7250 (t80) REVERT: D 1122 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7034 (mmt180) REVERT: D 1168 TRP cc_start: 0.6226 (OUTLIER) cc_final: 0.5359 (m100) REVERT: D 1210 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8218 (tpt170) REVERT: D 1271 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: E 472 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7983 (p90) REVERT: G 191 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4389 (m-10) REVERT: G 314 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7191 (mm-30) REVERT: G 351 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8459 (tp) REVERT: H 121 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.5987 (mp0) REVERT: H 434 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7316 (ptt90) REVERT: H 789 ILE cc_start: 0.7503 (tt) cc_final: 0.7133 (pt) REVERT: H 829 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.3466 (t70) REVERT: I 101 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: I 131 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: I 165 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8817 (pptt) REVERT: I 220 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: I 228 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.7131 (t-90) REVERT: K 151 ASN cc_start: 0.8840 (t0) cc_final: 0.8515 (t0) REVERT: K 303 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7864 (ptp90) REVERT: K 324 ILE cc_start: 0.7583 (tp) cc_final: 0.7337 (tt) REVERT: L 79 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: L 131 TRP cc_start: 0.8195 (t60) cc_final: 0.7364 (t60) REVERT: L 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6611 (mp0) REVERT: M 267 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8454 (mm-30) REVERT: N 139 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.8005 (mmm) REVERT: N 345 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8202 (mt) REVERT: N 377 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8338 (tt) REVERT: N 397 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7920 (pp20) REVERT: N 421 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.4993 (tp) REVERT: N 449 HIS cc_start: 0.7545 (m90) cc_final: 0.7089 (m90) REVERT: N 546 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6292 (pp20) REVERT: O 47 ILE cc_start: 0.8570 (mt) cc_final: 0.8347 (mt) REVERT: O 154 ASN cc_start: 0.7734 (m110) cc_final: 0.7225 (m110) REVERT: P 86 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7867 (pm20) REVERT: P 97 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8719 (ttt180) REVERT: P 122 ASN cc_start: 0.8582 (m-40) cc_final: 0.8047 (p0) REVERT: R 110 MET cc_start: 0.5212 (tpp) cc_final: 0.4619 (mtt) REVERT: S 265 MET cc_start: 0.2531 (pmm) cc_final: 0.1952 (pmm) REVERT: S 277 MET cc_start: 0.1485 (mtt) cc_final: 0.0507 (ttt) REVERT: S 303 GLN cc_start: 0.3810 (OUTLIER) cc_final: 0.3029 (mp10) REVERT: S 304 MET cc_start: 0.5120 (tpp) cc_final: 0.4569 (tpp) REVERT: S 340 MET cc_start: 0.4604 (mmm) cc_final: 0.3486 (mmm) REVERT: S 427 GLN cc_start: 0.2939 (OUTLIER) cc_final: 0.2447 (pt0) REVERT: S 429 PHE cc_start: -0.2500 (OUTLIER) cc_final: -0.2744 (m-10) REVERT: S 481 PHE cc_start: -0.0313 (OUTLIER) cc_final: -0.1870 (m-80) REVERT: S 498 ARG cc_start: 0.4366 (tpt170) cc_final: 0.4098 (ttt180) REVERT: S 509 ASP cc_start: 0.6959 (t0) cc_final: 0.6307 (m-30) REVERT: S 514 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6352 (tm-30) REVERT: J 401 ASP cc_start: 0.3080 (OUTLIER) cc_final: 0.1421 (m-30) REVERT: J 469 PHE cc_start: -0.0439 (m-80) cc_final: -0.0909 (m-80) REVERT: J 713 MET cc_start: 0.5237 (tmm) cc_final: 0.4990 (tmm) outliers start: 314 outliers final: 206 residues processed: 927 average time/residue: 0.5658 time to fit residues: 888.8281 Evaluate side-chains 899 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 647 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 889 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 941 ILE Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1122 ARG Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1168 TRP Chi-restraints excluded: chain D residue 1189 ILE Chi-restraints excluded: chain D residue 1200 ILE Chi-restraints excluded: chain D residue 1210 ARG Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1271 GLU Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 277 MET Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 466 TYR Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 734 LEU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 783 VAL Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 427 GLU Chi-restraints excluded: chain I residue 459 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 196 THR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain L residue 168 THR Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 495 GLU Chi-restraints excluded: chain N residue 506 LEU Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 534 ILE Chi-restraints excluded: chain N residue 546 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 97 ARG Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 MET Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain R residue 141 ASP Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 316 THR Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 429 PHE Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 496 LEU Chi-restraints excluded: chain S residue 514 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 401 ASP Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 612 optimal weight: 7.9990 chunk 303 optimal weight: 0.9980 chunk 550 optimal weight: 3.9990 chunk 560 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 346 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 726 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 414 HIS B 483 ASN B 540 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 229 ASN L 219 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN ** J 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125745 restraints weight = 95455.908| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.83 r_work: 0.3398 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 60283 Z= 0.188 Angle : 0.618 12.006 81662 Z= 0.321 Chirality : 0.044 0.227 8936 Planarity : 0.005 0.098 10667 Dihedral : 5.730 112.452 8239 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.79 % Favored : 88.70 % Rotamer: Outliers : 3.91 % Allowed : 25.93 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.10), residues: 7454 helix: 0.21 (0.11), residues: 2432 sheet: -1.39 (0.18), residues: 908 loop : -2.40 (0.09), residues: 4114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 131 HIS 0.006 0.001 HIS D 449 PHE 0.058 0.001 PHE D1170 TYR 0.027 0.001 TYR B 679 ARG 0.008 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 710 time to evaluate : 5.137 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: A 89 MET cc_start: 0.8483 (mmp) cc_final: 0.8277 (mmm) REVERT: B 55 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: B 71 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: B 127 LEU cc_start: 0.8493 (mt) cc_final: 0.8248 (pp) REVERT: B 154 TRP cc_start: 0.7179 (m100) cc_final: 0.6833 (m100) REVERT: B 169 TRP cc_start: 0.4837 (OUTLIER) cc_final: 0.4255 (p90) REVERT: B 171 ARG cc_start: 0.4883 (tpp80) cc_final: 0.4405 (tpp80) REVERT: B 178 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7534 (tp) REVERT: B 276 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6359 (tm-30) REVERT: B 503 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8608 (mt0) REVERT: B 589 TYR cc_start: 0.7945 (t80) cc_final: 0.7682 (t80) REVERT: B 948 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9000 (mt) REVERT: B 961 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6386 (ttt-90) REVERT: B 988 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7971 (mtt) REVERT: B 1010 SER cc_start: 0.7920 (m) cc_final: 0.7395 (p) REVERT: B 1014 LYS cc_start: 0.7635 (tttt) cc_final: 0.6780 (ttmt) REVERT: B 1045 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7968 (pm20) REVERT: B 1052 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7716 (mt-10) REVERT: C 239 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7135 (mtm-85) REVERT: C 514 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8317 (m-80) REVERT: C 533 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: C 573 TYR cc_start: 0.1028 (OUTLIER) cc_final: -0.0075 (m-10) REVERT: D 231 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7518 (mm-40) REVERT: D 328 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 1168 TRP cc_start: 0.6273 (OUTLIER) cc_final: 0.5224 (m100) REVERT: E 207 MET cc_start: 0.9006 (mtp) cc_final: 0.8655 (mtp) REVERT: E 472 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.7843 (p90) REVERT: G 191 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.4676 (m-10) REVERT: H 434 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7119 (ptt90) REVERT: H 789 ILE cc_start: 0.7508 (tt) cc_final: 0.7253 (pt) REVERT: H 790 MET cc_start: 0.7074 (tmm) cc_final: 0.6253 (ttt) REVERT: H 829 HIS cc_start: 0.5048 (OUTLIER) cc_final: 0.3466 (t70) REVERT: I 101 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: I 131 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: I 220 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6774 (tp30) REVERT: I 228 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7291 (t-90) REVERT: I 334 GLN cc_start: 0.6842 (tp-100) cc_final: 0.6611 (tp-100) REVERT: K 151 ASN cc_start: 0.8955 (t0) cc_final: 0.8698 (t0) REVERT: K 303 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8036 (ptp90) REVERT: L 131 TRP cc_start: 0.8067 (t60) cc_final: 0.7248 (t60) REVERT: L 219 ASN cc_start: 0.6814 (OUTLIER) cc_final: 0.6022 (m-40) REVERT: L 235 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: N 139 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (mmm) REVERT: N 345 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8189 (mt) REVERT: N 377 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (tt) REVERT: N 397 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: N 421 LEU cc_start: 0.5111 (OUTLIER) cc_final: 0.4815 (tp) REVERT: N 449 HIS cc_start: 0.7522 (m90) cc_final: 0.7046 (m90) REVERT: O 47 ILE cc_start: 0.8501 (mt) cc_final: 0.8277 (mt) REVERT: O 154 ASN cc_start: 0.7785 (m110) cc_final: 0.7292 (m110) REVERT: P 86 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: R 110 MET cc_start: 0.4921 (tpp) cc_final: 0.4326 (mtt) REVERT: R 142 MET cc_start: 0.4072 (mmm) cc_final: 0.3216 (mmm) REVERT: S 265 MET cc_start: 0.2555 (pmm) cc_final: 0.2048 (pmm) REVERT: S 277 MET cc_start: 0.1922 (mtt) cc_final: 0.0664 (ttt) REVERT: S 340 MET cc_start: 0.4479 (mmm) cc_final: 0.3502 (mmm) REVERT: S 427 GLN cc_start: 0.2626 (OUTLIER) cc_final: 0.2401 (pt0) REVERT: S 481 PHE cc_start: -0.1005 (OUTLIER) cc_final: -0.2443 (m-80) REVERT: S 485 MET cc_start: 0.1496 (ttt) cc_final: 0.1022 (tmm) REVERT: S 498 ARG cc_start: 0.4776 (tpt170) cc_final: 0.4323 (ttt180) REVERT: S 514 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: J 469 PHE cc_start: -0.0740 (m-80) cc_final: -0.1034 (m-80) REVERT: J 650 MET cc_start: 0.1628 (tpp) cc_final: 0.1191 (mtt) outliers start: 241 outliers final: 165 residues processed: 902 average time/residue: 0.5575 time to fit residues: 855.0878 Evaluate side-chains 878 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 679 time to evaluate : 5.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 231 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1168 TRP Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 734 LEU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 783 VAL Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 235 GLU Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 459 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 179 MET Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 546 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 317 VAL Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 374 ASP Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 514 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 325 ILE Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 678 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 662 optimal weight: 0.9980 chunk 490 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 561 optimal weight: 4.9990 chunk 508 optimal weight: 2.9990 chunk 537 optimal weight: 1.9990 chunk 251 optimal weight: 30.0000 chunk 502 optimal weight: 10.0000 chunk 365 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 414 HIS B 483 ASN B 540 ASN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN K 229 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN J 427 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.175347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.125101 restraints weight = 95460.381| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.91 r_work: 0.3372 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 60283 Z= 0.252 Angle : 0.636 9.980 81662 Z= 0.329 Chirality : 0.045 0.232 8936 Planarity : 0.005 0.098 10667 Dihedral : 5.684 112.288 8234 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.76 % Favored : 87.73 % Rotamer: Outliers : 3.83 % Allowed : 26.11 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.10), residues: 7454 helix: 0.21 (0.11), residues: 2431 sheet: -1.40 (0.18), residues: 915 loop : -2.38 (0.09), residues: 4108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 88 HIS 0.008 0.001 HIS P 129 PHE 0.059 0.001 PHE D1170 TYR 0.023 0.001 TYR B 679 ARG 0.014 0.000 ARG N 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 677 time to evaluate : 5.202 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: A 89 MET cc_start: 0.8316 (mmp) cc_final: 0.8112 (mmm) REVERT: A 114 ARG cc_start: 0.6854 (mmm-85) cc_final: 0.6325 (ttt180) REVERT: B 55 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: B 71 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: B 154 TRP cc_start: 0.7196 (m100) cc_final: 0.6843 (m100) REVERT: B 169 TRP cc_start: 0.4792 (OUTLIER) cc_final: 0.4232 (p90) REVERT: B 171 ARG cc_start: 0.4850 (tpp80) cc_final: 0.4373 (tpp80) REVERT: B 178 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7519 (tp) REVERT: B 256 CYS cc_start: 0.7985 (m) cc_final: 0.7532 (m) REVERT: B 961 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6571 (ttt-90) REVERT: B 988 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7891 (mtt) REVERT: B 1010 SER cc_start: 0.8010 (m) cc_final: 0.7626 (p) REVERT: B 1014 LYS cc_start: 0.7803 (tttt) cc_final: 0.6946 (ttmt) REVERT: B 1045 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7785 (pm20) REVERT: B 1052 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 80 GLU cc_start: 0.2491 (OUTLIER) cc_final: 0.2091 (tt0) REVERT: C 514 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: C 533 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: C 548 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7913 (mmp-170) REVERT: C 573 TYR cc_start: 0.0974 (OUTLIER) cc_final: -0.0254 (m-10) REVERT: D 157 GLN cc_start: 0.8351 (pm20) cc_final: 0.7672 (pp30) REVERT: D 231 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7407 (mm-40) REVERT: D 1168 TRP cc_start: 0.6210 (OUTLIER) cc_final: 0.5240 (m100) REVERT: E 207 MET cc_start: 0.8861 (mtp) cc_final: 0.8557 (mtp) REVERT: E 472 TRP cc_start: 0.8475 (OUTLIER) cc_final: 0.7724 (p90) REVERT: G 191 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.4631 (m-10) REVERT: G 244 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: H 121 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.5969 (mp0) REVERT: H 434 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7283 (ptt90) REVERT: H 789 ILE cc_start: 0.7347 (tt) cc_final: 0.7063 (pt) REVERT: H 790 MET cc_start: 0.6944 (tmm) cc_final: 0.6029 (ttt) REVERT: H 829 HIS cc_start: 0.5093 (OUTLIER) cc_final: 0.3553 (t70) REVERT: I 101 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: I 131 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: I 220 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6748 (tp30) REVERT: I 228 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7196 (t-90) REVERT: K 151 ASN cc_start: 0.8893 (t0) cc_final: 0.8619 (t0) REVERT: K 303 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7856 (ptp90) REVERT: L 79 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: L 131 TRP cc_start: 0.8131 (t60) cc_final: 0.7157 (t60) REVERT: L 235 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: N 139 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7892 (mmm) REVERT: N 345 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8176 (mt) REVERT: N 377 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8334 (tt) REVERT: N 397 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7897 (pp20) REVERT: N 421 LEU cc_start: 0.5165 (OUTLIER) cc_final: 0.4849 (tp) REVERT: N 449 HIS cc_start: 0.7477 (m90) cc_final: 0.7023 (m90) REVERT: O 47 ILE cc_start: 0.8555 (mt) cc_final: 0.8311 (mt) REVERT: O 154 ASN cc_start: 0.7700 (m110) cc_final: 0.7196 (m110) REVERT: P 86 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: R 142 MET cc_start: 0.4561 (mmm) cc_final: 0.3441 (mmm) REVERT: S 265 MET cc_start: 0.2488 (pmm) cc_final: 0.1986 (pmm) REVERT: S 277 MET cc_start: 0.2031 (mtt) cc_final: 0.0683 (ttt) REVERT: S 340 MET cc_start: 0.4699 (mmm) cc_final: 0.3645 (mmm) REVERT: S 427 GLN cc_start: 0.2826 (OUTLIER) cc_final: 0.2413 (pt0) REVERT: S 429 PHE cc_start: -0.2328 (OUTLIER) cc_final: -0.2604 (m-10) REVERT: S 481 PHE cc_start: -0.0896 (OUTLIER) cc_final: -0.2347 (m-80) REVERT: S 498 ARG cc_start: 0.4626 (tpt170) cc_final: 0.4393 (ttt180) REVERT: S 514 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6339 (tm-30) REVERT: S 528 GLN cc_start: 0.6592 (mm-40) cc_final: 0.6192 (mm-40) REVERT: J 469 PHE cc_start: -0.0861 (m-80) cc_final: -0.1209 (m-80) REVERT: J 650 MET cc_start: 0.1799 (tpp) cc_final: 0.1236 (mtt) outliers start: 236 outliers final: 173 residues processed: 865 average time/residue: 0.6002 time to fit residues: 885.2140 Evaluate side-chains 870 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 661 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1168 TRP Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 244 GLU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 734 LEU Chi-restraints excluded: chain H residue 752 GLU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 783 VAL Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 235 GLU Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 459 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 489 LEU Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 546 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain S residue 197 TRP Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 374 ASP Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 429 PHE Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 496 LEU Chi-restraints excluded: chain S residue 514 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 608 optimal weight: 0.9980 chunk 641 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 398 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 489 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 429 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN B 540 ASN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 373 ASN K 229 ASN ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN J 427 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125545 restraints weight = 95917.351| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.87 r_work: 0.3380 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 60283 Z= 0.254 Angle : 0.687 59.112 81662 Z= 0.367 Chirality : 0.045 0.287 8936 Planarity : 0.005 0.098 10667 Dihedral : 5.681 112.304 8234 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.78 % Favored : 87.69 % Rotamer: Outliers : 3.65 % Allowed : 26.35 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.10), residues: 7454 helix: 0.22 (0.11), residues: 2430 sheet: -1.40 (0.18), residues: 915 loop : -2.37 (0.09), residues: 4109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 88 HIS 0.007 0.001 HIS D 449 PHE 0.045 0.001 PHE D1170 TYR 0.039 0.001 TYR D1251 ARG 0.011 0.000 ARG N 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14908 Ramachandran restraints generated. 7454 Oldfield, 0 Emsley, 7454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 661 time to evaluate : 5.223 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: A 89 MET cc_start: 0.8312 (mmp) cc_final: 0.8107 (mmm) REVERT: A 114 ARG cc_start: 0.6853 (mmm-85) cc_final: 0.6324 (ttt180) REVERT: B 55 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: B 71 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: B 154 TRP cc_start: 0.7210 (m100) cc_final: 0.6942 (m100) REVERT: B 169 TRP cc_start: 0.4796 (OUTLIER) cc_final: 0.4235 (p90) REVERT: B 171 ARG cc_start: 0.4851 (tpp80) cc_final: 0.4378 (tpp80) REVERT: B 178 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7517 (tp) REVERT: B 256 CYS cc_start: 0.7981 (m) cc_final: 0.7527 (m) REVERT: B 948 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8976 (mt) REVERT: B 961 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6572 (ttt-90) REVERT: B 988 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7881 (mtt) REVERT: B 1010 SER cc_start: 0.8001 (m) cc_final: 0.7623 (p) REVERT: B 1014 LYS cc_start: 0.7811 (tttt) cc_final: 0.6949 (ttmt) REVERT: B 1045 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: B 1052 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7645 (mt-10) REVERT: C 80 GLU cc_start: 0.2484 (OUTLIER) cc_final: 0.2088 (tt0) REVERT: C 514 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: C 533 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: C 548 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7897 (mmp-170) REVERT: C 573 TYR cc_start: 0.0984 (OUTLIER) cc_final: -0.0253 (m-10) REVERT: D 157 GLN cc_start: 0.8360 (pm20) cc_final: 0.7667 (pp30) REVERT: D 231 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7406 (mm-40) REVERT: D 1168 TRP cc_start: 0.6201 (OUTLIER) cc_final: 0.5230 (m100) REVERT: E 207 MET cc_start: 0.8877 (mtp) cc_final: 0.8549 (mtp) REVERT: E 472 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7696 (p90) REVERT: G 191 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.4617 (m-10) REVERT: G 244 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: H 121 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: H 434 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7306 (ptt90) REVERT: H 510 TYR cc_start: 0.5896 (p90) cc_final: 0.5326 (p90) REVERT: H 789 ILE cc_start: 0.7342 (tt) cc_final: 0.7065 (pt) REVERT: H 790 MET cc_start: 0.6936 (tmm) cc_final: 0.6021 (ttt) REVERT: H 829 HIS cc_start: 0.5092 (OUTLIER) cc_final: 0.3551 (t70) REVERT: I 101 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: I 131 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: I 220 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: I 228 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7200 (t-90) REVERT: I 434 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7331 (tp30) REVERT: K 151 ASN cc_start: 0.8892 (t0) cc_final: 0.8636 (t0) REVERT: K 303 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7840 (ptp90) REVERT: L 79 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: L 131 TRP cc_start: 0.8127 (t60) cc_final: 0.7160 (t60) REVERT: L 235 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: N 139 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7884 (mmm) REVERT: N 345 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8168 (mt) REVERT: N 377 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8326 (tt) REVERT: N 397 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7896 (pp20) REVERT: N 421 LEU cc_start: 0.5166 (OUTLIER) cc_final: 0.4849 (tp) REVERT: N 449 HIS cc_start: 0.7470 (m90) cc_final: 0.7012 (m90) REVERT: O 47 ILE cc_start: 0.8553 (mt) cc_final: 0.8312 (mt) REVERT: O 154 ASN cc_start: 0.7687 (m110) cc_final: 0.7180 (m110) REVERT: P 86 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: R 110 MET cc_start: 0.5395 (tpp) cc_final: 0.4600 (mtt) REVERT: R 142 MET cc_start: 0.4483 (mmm) cc_final: 0.3440 (mmm) REVERT: S 265 MET cc_start: 0.2487 (pmm) cc_final: 0.1984 (pmm) REVERT: S 277 MET cc_start: 0.2034 (mtt) cc_final: 0.0680 (ttt) REVERT: S 301 MET cc_start: 0.1839 (tpp) cc_final: 0.1631 (tpp) REVERT: S 340 MET cc_start: 0.4678 (mmm) cc_final: 0.3620 (mmm) REVERT: S 427 GLN cc_start: 0.2817 (OUTLIER) cc_final: 0.2410 (pt0) REVERT: S 429 PHE cc_start: -0.2327 (OUTLIER) cc_final: -0.2600 (m-10) REVERT: S 481 PHE cc_start: -0.0894 (OUTLIER) cc_final: -0.2345 (m-80) REVERT: S 498 ARG cc_start: 0.4680 (tpt170) cc_final: 0.4372 (ttt180) REVERT: S 514 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6330 (tm-30) REVERT: J 306 VAL cc_start: 0.3449 (OUTLIER) cc_final: 0.3249 (p) REVERT: J 469 PHE cc_start: -0.0848 (m-80) cc_final: -0.1191 (m-80) REVERT: J 650 MET cc_start: 0.1798 (tpp) cc_final: 0.1237 (mtt) outliers start: 225 outliers final: 177 residues processed: 840 average time/residue: 0.5688 time to fit residues: 810.3277 Evaluate side-chains 873 residues out of total 6578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 658 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 631 CYS Chi-restraints excluded: chain B residue 672 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 829 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain B residue 961 ARG Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1008 TYR Chi-restraints excluded: chain B residue 1012 HIS Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 106 TYR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 393 HIS Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 517 MET Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 573 TYR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 1051 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1126 ILE Chi-restraints excluded: chain D residue 1130 LEU Chi-restraints excluded: chain D residue 1150 GLU Chi-restraints excluded: chain D residue 1168 TRP Chi-restraints excluded: chain D residue 1232 LEU Chi-restraints excluded: chain D residue 1254 THR Chi-restraints excluded: chain D residue 1258 ILE Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1300 VAL Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 333 TYR Chi-restraints excluded: chain E residue 385 VAL Chi-restraints excluded: chain E residue 472 TRP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 181 MET Chi-restraints excluded: chain G residue 191 TYR Chi-restraints excluded: chain G residue 244 GLU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain G residue 411 HIS Chi-restraints excluded: chain G residue 422 LYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 115 HIS Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 457 LEU Chi-restraints excluded: chain H residue 486 HIS Chi-restraints excluded: chain H residue 492 HIS Chi-restraints excluded: chain H residue 734 LEU Chi-restraints excluded: chain H residue 761 TRP Chi-restraints excluded: chain H residue 765 TRP Chi-restraints excluded: chain H residue 769 LEU Chi-restraints excluded: chain H residue 783 VAL Chi-restraints excluded: chain H residue 801 THR Chi-restraints excluded: chain H residue 829 HIS Chi-restraints excluded: chain H residue 833 TYR Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 144 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 220 GLU Chi-restraints excluded: chain I residue 223 MET Chi-restraints excluded: chain I residue 228 HIS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 235 GLU Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 267 CYS Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 305 PHE Chi-restraints excluded: chain I residue 332 SER Chi-restraints excluded: chain I residue 350 ASN Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 373 ASN Chi-restraints excluded: chain I residue 381 TYR Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 408 THR Chi-restraints excluded: chain I residue 459 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 489 LEU Chi-restraints excluded: chain K residue 113 THR Chi-restraints excluded: chain K residue 138 ASP Chi-restraints excluded: chain K residue 229 ASN Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 303 ARG Chi-restraints excluded: chain K residue 323 TRP Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 223 TRP Chi-restraints excluded: chain L residue 233 VAL Chi-restraints excluded: chain L residue 235 GLU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 139 PHE Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 272 VAL Chi-restraints excluded: chain N residue 136 MET Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 220 MET Chi-restraints excluded: chain N residue 281 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 466 THR Chi-restraints excluded: chain N residue 530 LEU Chi-restraints excluded: chain N residue 546 GLU Chi-restraints excluded: chain O residue 16 LYS Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain P residue 83 LYS Chi-restraints excluded: chain P residue 86 GLU Chi-restraints excluded: chain P residue 158 PHE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 103 TRP Chi-restraints excluded: chain S residue 197 TRP Chi-restraints excluded: chain S residue 201 VAL Chi-restraints excluded: chain S residue 226 ILE Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 312 LEU Chi-restraints excluded: chain S residue 370 VAL Chi-restraints excluded: chain S residue 374 ASP Chi-restraints excluded: chain S residue 379 LEU Chi-restraints excluded: chain S residue 382 TRP Chi-restraints excluded: chain S residue 388 THR Chi-restraints excluded: chain S residue 400 ASP Chi-restraints excluded: chain S residue 413 CYS Chi-restraints excluded: chain S residue 420 GLU Chi-restraints excluded: chain S residue 427 GLN Chi-restraints excluded: chain S residue 429 PHE Chi-restraints excluded: chain S residue 442 LEU Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 460 HIS Chi-restraints excluded: chain S residue 481 PHE Chi-restraints excluded: chain S residue 492 LEU Chi-restraints excluded: chain S residue 496 LEU Chi-restraints excluded: chain S residue 514 GLU Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 348 MET Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 583 CYS Chi-restraints excluded: chain J residue 585 VAL Chi-restraints excluded: chain J residue 626 SER Chi-restraints excluded: chain J residue 675 THR Chi-restraints excluded: chain J residue 688 TYR Chi-restraints excluded: chain J residue 691 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 741 random chunks: chunk 427 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 656 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 693 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 614 optimal weight: 10.0000 chunk 686 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 740 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 483 ASN ** B 711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN ** C 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125409 restraints weight = 95961.802| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.86 r_work: 0.3380 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1485 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.446 60283 Z= 0.352 Angle : 0.667 39.347 81662 Z= 0.369 Chirality : 0.045 0.546 8936 Planarity : 0.005 0.254 10667 Dihedral : 5.515 71.716 8231 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.78 % Favored : 87.69 % Rotamer: Outliers : 3.54 % Allowed : 26.50 % Favored : 69.97 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.10), residues: 7454 helix: 0.22 (0.11), residues: 2430 sheet: -1.40 (0.18), residues: 915 loop : -2.38 (0.09), residues: 4109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 88 HIS 0.007 0.001 HIS D 449 PHE 0.045 0.001 PHE D1170 TYR 0.039 0.001 TYR D1251 ARG 0.011 0.000 ARG N 507 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36582.96 seconds wall clock time: 626 minutes 15.95 seconds (37575.95 seconds total)