Starting phenix.real_space_refine on Tue Aug 26 11:51:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.map" model { file = "/net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9q_51971/08_2025/9h9q_51971.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 23514 2.51 5 N 6100 2.21 5 O 6886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36618 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3188 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3220 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 387} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6001 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 720} Chain breaks: 4 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 5313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5313 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 314 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "F" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 273 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3220 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 16, 'TRANS': 387} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 5313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5313 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 620} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3188 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 5 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 6001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6001 Classifications: {'peptide': 735} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 720} Chain breaks: 4 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "K" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 314 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "L" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 273 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Time building chain proxies: 7.33, per 1000 atoms: 0.20 Number of scatterers: 36618 At special positions: 0 Unit cell: (156.22, 175.48, 225.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 6886 8.00 N 6100 7.00 C 23514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8628 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 22 sheets defined 66.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 Processing helix chain 'A' and resid 76 through 79 removed outlier: 3.607A pdb=" N LEU A 79 " --> pdb=" O HIS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 99 through 110 removed outlier: 4.315A pdb=" N ILE A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 141 through 156 removed outlier: 3.587A pdb=" N GLU A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 189 Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.896A pdb=" N ARG A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.837A pdb=" N ILE A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.681A pdb=" N ASN A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'A' and resid 329 through 334 removed outlier: 5.943A pdb=" N ARG A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.918A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 436 through 466 removed outlier: 3.711A pdb=" N LYS A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 removed outlier: 3.724A pdb=" N GLN B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 removed outlier: 3.579A pdb=" N LEU B 79 " --> pdb=" O HIS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 99 through 110 removed outlier: 4.371A pdb=" N ILE B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.669A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 188 removed outlier: 3.685A pdb=" N TYR B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.740A pdb=" N ARG B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.694A pdb=" N ILE B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 320 through 329 removed outlier: 4.106A pdb=" N SER B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 372 removed outlier: 3.929A pdb=" N GLN B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.676A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 464 removed outlier: 3.547A pdb=" N ILE B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 removed outlier: 4.000A pdb=" N PHE C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 134 through 162 removed outlier: 4.445A pdb=" N LYS C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 198 removed outlier: 4.210A pdb=" N VAL C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 214 through 236 Processing helix chain 'C' and resid 278 through 288 removed outlier: 3.503A pdb=" N VAL C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 322 removed outlier: 3.533A pdb=" N SER C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 342 through 349 Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.656A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 371 through 393 Processing helix chain 'C' and resid 414 through 437 Processing helix chain 'C' and resid 439 through 453 removed outlier: 3.509A pdb=" N ASN C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.680A pdb=" N LYS C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 removed outlier: 4.003A pdb=" N ILE C 477 " --> pdb=" O LYS C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.371A pdb=" N LEU C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 483 " --> pdb=" O VAL C 479 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 510 removed outlier: 4.064A pdb=" N LYS C 510 " --> pdb=" O ASP C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.759A pdb=" N GLU C 526 " --> pdb=" O TYR C 522 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 528 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 578 Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.956A pdb=" N VAL C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 629 through 634 Processing helix chain 'C' and resid 638 through 669 Processing helix chain 'C' and resid 670 through 691 removed outlier: 3.557A pdb=" N ASN C 674 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU C 677 " --> pdb=" O HIS C 673 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 678 " --> pdb=" O ASN C 674 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR C 691 " --> pdb=" O THR C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 711 removed outlier: 4.751A pdb=" N ILE C 711 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 725 removed outlier: 3.644A pdb=" N ASP C 722 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 723 " --> pdb=" O SER C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 758 removed outlier: 3.648A pdb=" N PHE C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 794 removed outlier: 3.571A pdb=" N LYS C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS C 788 " --> pdb=" O VAL C 784 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 789 " --> pdb=" O GLN C 785 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 791 " --> pdb=" O LYS C 787 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 792 " --> pdb=" O LYS C 788 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 793 " --> pdb=" O VAL C 789 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 794 " --> pdb=" O LEU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 803 removed outlier: 3.621A pdb=" N PHE C 798 " --> pdb=" O ASN C 794 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 854 Processing helix chain 'C' and resid 855 through 869 removed outlier: 3.818A pdb=" N LEU C 859 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 860 " --> pdb=" O GLN C 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 3.545A pdb=" N LEU D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 133 through 138' Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.527A pdb=" N TYR D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) Proline residue: D 155 - end of helix Processing helix chain 'D' and resid 182 through 209 removed outlier: 3.793A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU D 194 " --> pdb=" O ARG D 190 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 242 Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.642A pdb=" N VAL D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 removed outlier: 3.835A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.631A pdb=" N LEU D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 291 through 319 removed outlier: 3.620A pdb=" N THR D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 304 " --> pdb=" O THR D 300 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 348 through 351 removed outlier: 3.712A pdb=" N ILE D 351 " --> pdb=" O PRO D 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 357 through 374 removed outlier: 3.838A pdb=" N GLN D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 393 removed outlier: 3.695A pdb=" N ILE D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 427 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 447 through 458 removed outlier: 3.598A pdb=" N ILE D 451 " --> pdb=" O THR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 485 Processing helix chain 'D' and resid 486 through 490 removed outlier: 3.574A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 494 No H-bonds generated for 'chain 'D' and resid 492 through 494' Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.001A pdb=" N LEU D 527 " --> pdb=" O PRO D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 567 removed outlier: 3.645A pdb=" N HIS D 533 " --> pdb=" O GLU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 Processing helix chain 'D' and resid 572 through 608 removed outlier: 4.488A pdb=" N ARG D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) Proline residue: D 578 - end of helix Processing helix chain 'D' and resid 608 through 617 Processing helix chain 'D' and resid 617 through 622 Processing helix chain 'D' and resid 627 through 632 removed outlier: 4.112A pdb=" N LEU D 632 " --> pdb=" O GLN D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 637 removed outlier: 3.663A pdb=" N PHE D 636 " --> pdb=" O ASN D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 674 removed outlier: 3.627A pdb=" N ILE D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 723 removed outlier: 3.570A pdb=" N GLU D 711 " --> pdb=" O ASN D 707 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 723 " --> pdb=" O PHE D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 755 Processing helix chain 'D' and resid 760 through 774 removed outlier: 3.953A pdb=" N ARG D 774 " --> pdb=" O ASN D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 785 Processing helix chain 'E' and resid 238 through 266 Processing helix chain 'F' and resid 240 through 269 Processing helix chain 'G' and resid 11 through 29 removed outlier: 3.725A pdb=" N GLN G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 79 removed outlier: 3.580A pdb=" N LEU G 79 " --> pdb=" O HIS G 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 79' Processing helix chain 'G' and resid 99 through 110 removed outlier: 4.371A pdb=" N ILE G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'G' and resid 130 through 141 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.669A pdb=" N LEU G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS G 155 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 188 removed outlier: 3.685A pdb=" N TYR G 188 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 226 removed outlier: 3.740A pdb=" N ARG G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 243 Processing helix chain 'G' and resid 263 through 275 removed outlier: 3.694A pdb=" N ILE G 267 " --> pdb=" O ALA G 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER G 275 " --> pdb=" O SER G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 287 through 294 Processing helix chain 'G' and resid 320 through 329 removed outlier: 4.105A pdb=" N SER G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 372 removed outlier: 3.928A pdb=" N GLN G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 371 " --> pdb=" O LYS G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 425 removed outlier: 3.676A pdb=" N VAL G 412 " --> pdb=" O SER G 408 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 464 removed outlier: 3.547A pdb=" N ILE G 457 " --> pdb=" O SER G 453 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU G 460 " --> pdb=" O SER G 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 3.544A pdb=" N LEU H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 133 through 138' Processing helix chain 'H' and resid 139 through 142 Processing helix chain 'H' and resid 149 through 159 removed outlier: 3.526A pdb=" N TYR H 153 " --> pdb=" O THR H 149 " (cutoff:3.500A) Proline residue: H 155 - end of helix Processing helix chain 'H' and resid 182 through 209 removed outlier: 3.793A pdb=" N GLU H 191 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU H 194 " --> pdb=" O ARG H 190 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 242 Processing helix chain 'H' and resid 246 through 255 removed outlier: 3.642A pdb=" N VAL H 250 " --> pdb=" O SER H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 270 removed outlier: 3.834A pdb=" N ARG H 270 " --> pdb=" O ARG H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 285 removed outlier: 3.631A pdb=" N LEU H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 289 Processing helix chain 'H' and resid 291 through 319 removed outlier: 3.620A pdb=" N THR H 303 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU H 304 " --> pdb=" O THR H 300 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'H' and resid 339 through 343 Processing helix chain 'H' and resid 348 through 351 removed outlier: 3.712A pdb=" N ILE H 351 " --> pdb=" O PRO H 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 348 through 351' Processing helix chain 'H' and resid 357 through 374 removed outlier: 3.838A pdb=" N GLN H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 393 removed outlier: 3.695A pdb=" N ILE H 391 " --> pdb=" O LYS H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 427 Processing helix chain 'H' and resid 431 through 444 Processing helix chain 'H' and resid 447 through 458 removed outlier: 3.598A pdb=" N ILE H 451 " --> pdb=" O THR H 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 485 Processing helix chain 'H' and resid 486 through 490 removed outlier: 3.575A pdb=" N ASN H 489 " --> pdb=" O SER H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 492 through 494 No H-bonds generated for 'chain 'H' and resid 492 through 494' Processing helix chain 'H' and resid 508 through 511 Processing helix chain 'H' and resid 523 through 528 removed outlier: 4.001A pdb=" N LEU H 527 " --> pdb=" O PRO H 523 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 567 removed outlier: 3.645A pdb=" N HIS H 533 " --> pdb=" O GLU H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 568 through 571 Processing helix chain 'H' and resid 572 through 608 removed outlier: 4.488A pdb=" N ARG H 577 " --> pdb=" O SER H 573 " (cutoff:3.500A) Proline residue: H 578 - end of helix Processing helix chain 'H' and resid 608 through 617 Processing helix chain 'H' and resid 617 through 622 Processing helix chain 'H' and resid 627 through 632 removed outlier: 4.112A pdb=" N LEU H 632 " --> pdb=" O GLN H 628 " (cutoff:3.500A) Processing helix chain 'H' and resid 633 through 637 removed outlier: 3.663A pdb=" N PHE H 636 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 657 through 674 removed outlier: 3.628A pdb=" N ILE H 672 " --> pdb=" O TYR H 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 690 through 723 removed outlier: 3.571A pdb=" N GLU H 711 " --> pdb=" O ASN H 707 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 723 " --> pdb=" O PHE H 719 " (cutoff:3.500A) Processing helix chain 'H' and resid 737 through 755 Processing helix chain 'H' and resid 760 through 774 removed outlier: 3.954A pdb=" N ARG H 774 " --> pdb=" O ASN H 770 " (cutoff:3.500A) Processing helix chain 'H' and resid 778 through 785 Processing helix chain 'I' and resid 11 through 30 Processing helix chain 'I' and resid 76 through 79 removed outlier: 3.607A pdb=" N LEU I 79 " --> pdb=" O HIS I 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 76 through 79' Processing helix chain 'I' and resid 99 through 110 removed outlier: 4.315A pdb=" N ILE I 103 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 116 No H-bonds generated for 'chain 'I' and resid 114 through 116' Processing helix chain 'I' and resid 132 through 141 Processing helix chain 'I' and resid 141 through 156 removed outlier: 3.587A pdb=" N GLU I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 189 Processing helix chain 'I' and resid 212 through 227 removed outlier: 3.896A pdb=" N ARG I 222 " --> pdb=" O LEU I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 263 through 275 removed outlier: 3.837A pdb=" N ILE I 267 " --> pdb=" O ALA I 263 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER I 275 " --> pdb=" O SER I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 280 Processing helix chain 'I' and resid 287 through 294 removed outlier: 3.680A pdb=" N ASN I 294 " --> pdb=" O SER I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 328 Processing helix chain 'I' and resid 329 through 334 removed outlier: 5.943A pdb=" N ARG I 332 " --> pdb=" O SER I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 372 Processing helix chain 'I' and resid 408 through 426 removed outlier: 3.918A pdb=" N VAL I 412 " --> pdb=" O SER I 408 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG I 426 " --> pdb=" O LEU I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 433 Processing helix chain 'I' and resid 436 through 466 removed outlier: 3.704A pdb=" N LYS I 465 " --> pdb=" O TYR I 461 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU I 466 " --> pdb=" O LYS I 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 99 removed outlier: 4.000A pdb=" N PHE J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 124 Processing helix chain 'J' and resid 134 through 162 removed outlier: 4.445A pdb=" N LYS J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY J 148 " --> pdb=" O LEU J 144 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN J 159 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 160 " --> pdb=" O SER J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 165 No H-bonds generated for 'chain 'J' and resid 163 through 165' Processing helix chain 'J' and resid 166 through 198 removed outlier: 4.210A pdb=" N VAL J 170 " --> pdb=" O PHE J 166 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN J 186 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 214 Processing helix chain 'J' and resid 214 through 236 Processing helix chain 'J' and resid 278 through 288 removed outlier: 3.503A pdb=" N VAL J 288 " --> pdb=" O GLN J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 322 removed outlier: 3.534A pdb=" N SER J 309 " --> pdb=" O ASP J 305 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP J 310 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TYR J 311 " --> pdb=" O VAL J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'J' and resid 342 through 349 Processing helix chain 'J' and resid 349 through 357 removed outlier: 3.657A pdb=" N TYR J 353 " --> pdb=" O LYS J 349 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 357 " --> pdb=" O TYR J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 365 Processing helix chain 'J' and resid 371 through 393 Processing helix chain 'J' and resid 414 through 437 Processing helix chain 'J' and resid 439 through 453 removed outlier: 3.510A pdb=" N ASN J 445 " --> pdb=" O PRO J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 466 Processing helix chain 'J' and resid 466 through 471 removed outlier: 3.680A pdb=" N LYS J 471 " --> pdb=" O PHE J 467 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 477 removed outlier: 4.004A pdb=" N ILE J 477 " --> pdb=" O LYS J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 488 removed outlier: 4.371A pdb=" N LEU J 482 " --> pdb=" O SER J 478 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN J 483 " --> pdb=" O VAL J 479 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS J 484 " --> pdb=" O SER J 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 503 through 510 removed outlier: 4.064A pdb=" N LYS J 510 " --> pdb=" O ASP J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 528 removed outlier: 3.760A pdb=" N GLU J 526 " --> pdb=" O TYR J 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU J 528 " --> pdb=" O VAL J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 578 Processing helix chain 'J' and resid 589 through 594 removed outlier: 3.956A pdb=" N VAL J 593 " --> pdb=" O PRO J 589 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 629 Processing helix chain 'J' and resid 629 through 634 Processing helix chain 'J' and resid 638 through 669 Processing helix chain 'J' and resid 670 through 691 removed outlier: 3.557A pdb=" N ASN J 674 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU J 677 " --> pdb=" O HIS J 673 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE J 678 " --> pdb=" O ASN J 674 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR J 691 " --> pdb=" O THR J 687 " (cutoff:3.500A) Processing helix chain 'J' and resid 706 through 711 removed outlier: 4.750A pdb=" N ILE J 711 " --> pdb=" O ASN J 707 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 725 removed outlier: 3.832A pdb=" N ASP J 722 " --> pdb=" O ASN J 718 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER J 723 " --> pdb=" O SER J 719 " (cutoff:3.500A) Processing helix chain 'J' and resid 739 through 758 removed outlier: 3.648A pdb=" N PHE J 747 " --> pdb=" O LEU J 743 " (cutoff:3.500A) Processing helix chain 'J' and resid 762 through 794 removed outlier: 3.570A pdb=" N LYS J 787 " --> pdb=" O ILE J 783 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS J 788 " --> pdb=" O VAL J 784 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL J 789 " --> pdb=" O GLN J 785 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 791 " --> pdb=" O LYS J 787 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU J 792 " --> pdb=" O LYS J 788 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 793 " --> pdb=" O VAL J 789 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN J 794 " --> pdb=" O LEU J 790 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 803 removed outlier: 3.621A pdb=" N PHE J 798 " --> pdb=" O ASN J 794 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU J 800 " --> pdb=" O GLU J 796 " (cutoff:3.500A) Processing helix chain 'J' and resid 815 through 854 Processing helix chain 'J' and resid 855 through 869 removed outlier: 3.818A pdb=" N LEU J 859 " --> pdb=" O ASN J 855 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU J 860 " --> pdb=" O GLN J 856 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU J 861 " --> pdb=" O GLY J 857 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 266 Processing helix chain 'L' and resid 240 through 269 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.546A pdb=" N LEU A 95 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 4 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLN A 163 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE A 6 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 165 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 8 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 160 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ASN A 195 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE A 162 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 197 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 164 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 199 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 198 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 230 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER A 306 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 232 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ILE A 308 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 12.782A pdb=" N HIS A 234 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE A 303 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN A 406 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU A 399 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU A 351 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 401 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASN A 349 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 403 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N MET A 347 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 405 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A 385 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 349 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A 387 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 351 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 120 removed outlier: 8.302A pdb=" N HIS B 119 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 95 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE B 94 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR B 7 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE B 96 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN B 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU B 4 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 160 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN B 195 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 162 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 194 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE B 231 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 196 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE B 233 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 118 through 120 removed outlier: 8.302A pdb=" N HIS B 119 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 95 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE B 94 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR B 7 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE B 96 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN B 9 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU B 4 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER B 160 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN B 195 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 162 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 194 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE B 231 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR B 196 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE B 233 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N THR B 230 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER B 306 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 232 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N ILE B 308 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 12.837A pdb=" N HIS B 234 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE B 303 " --> pdb=" O ASN B 406 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN B 406 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 401 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN B 349 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 403 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N MET B 347 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN B 405 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 385 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN B 349 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 387 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU B 351 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.456A pdb=" N ASP C 39 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 174 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR D 167 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 109 Processing sheet with id=AA8, first strand: chain 'C' and resid 333 through 335 Processing sheet with id=AA9, first strand: chain 'C' and resid 513 through 516 Processing sheet with id=AB1, first strand: chain 'D' and resid 331 through 333 Processing sheet with id=AB2, first strand: chain 'D' and resid 513 through 517 Processing sheet with id=AB3, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AB4, first strand: chain 'G' and resid 118 through 120 removed outlier: 8.302A pdb=" N HIS G 119 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU G 95 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE G 94 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR G 7 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE G 96 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN G 9 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU G 4 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER G 160 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN G 195 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE G 162 " --> pdb=" O ASN G 195 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 194 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE G 231 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 196 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE G 233 " --> pdb=" O THR G 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 118 through 120 removed outlier: 8.302A pdb=" N HIS G 119 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU G 95 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE G 94 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR G 7 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE G 96 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN G 9 " --> pdb=" O ILE G 96 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU G 4 " --> pdb=" O LEU G 159 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER G 160 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASN G 195 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE G 162 " --> pdb=" O ASN G 195 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU G 194 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE G 231 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 196 " --> pdb=" O PHE G 231 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE G 233 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N THR G 230 " --> pdb=" O LEU G 304 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER G 306 " --> pdb=" O THR G 230 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL G 232 " --> pdb=" O SER G 306 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N ILE G 308 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 12.837A pdb=" N HIS G 234 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE G 303 " --> pdb=" O ASN G 406 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN G 406 " --> pdb=" O PHE G 303 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE G 401 " --> pdb=" O ASN G 349 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASN G 349 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL G 403 " --> pdb=" O MET G 347 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N MET G 347 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN G 405 " --> pdb=" O ILE G 345 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL G 385 " --> pdb=" O MET G 347 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN G 349 " --> pdb=" O VAL G 385 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY G 387 " --> pdb=" O ASN G 349 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU G 351 " --> pdb=" O GLY G 387 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AB7, first strand: chain 'H' and resid 167 through 169 removed outlier: 4.208A pdb=" N THR H 167 " --> pdb=" O GLU H 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 174 " --> pdb=" O SER H 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 331 through 333 Processing sheet with id=AB9, first strand: chain 'I' and resid 118 through 119 removed outlier: 6.547A pdb=" N LEU I 95 " --> pdb=" O HIS I 119 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU I 4 " --> pdb=" O ASN I 161 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLN I 163 " --> pdb=" O GLU I 4 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE I 6 " --> pdb=" O GLN I 163 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE I 165 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU I 8 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER I 160 " --> pdb=" O LEU I 193 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASN I 195 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE I 162 " --> pdb=" O ASN I 195 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE I 197 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU I 164 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE I 199 " --> pdb=" O LEU I 164 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER I 198 " --> pdb=" O PHE I 231 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR I 230 " --> pdb=" O LEU I 304 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER I 306 " --> pdb=" O THR I 230 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL I 232 " --> pdb=" O SER I 306 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ILE I 308 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 12.781A pdb=" N HIS I 234 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE I 303 " --> pdb=" O ASN I 406 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN I 406 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU I 399 " --> pdb=" O LEU I 351 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU I 351 " --> pdb=" O GLU I 399 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE I 401 " --> pdb=" O ASN I 349 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN I 349 " --> pdb=" O ILE I 401 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL I 403 " --> pdb=" O MET I 347 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N MET I 347 " --> pdb=" O VAL I 403 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN I 405 " --> pdb=" O ILE I 345 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL I 385 " --> pdb=" O MET I 347 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN I 349 " --> pdb=" O VAL I 385 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY I 387 " --> pdb=" O ASN I 349 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU I 351 " --> pdb=" O GLY I 387 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AC2, first strand: chain 'J' and resid 107 through 109 Processing sheet with id=AC3, first strand: chain 'J' and resid 333 through 335 Processing sheet with id=AC4, first strand: chain 'J' and resid 513 through 516 2090 hydrogen bonds defined for protein. 6168 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: 8.14 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6082 1.28 - 1.42: 9332 1.42 - 1.55: 21688 1.55 - 1.68: 8 1.68 - 1.81: 208 Bond restraints: 37318 Sorted by residual: bond pdb=" C HIS A 316 " pdb=" O HIS A 316 " ideal model delta sigma weight residual 1.230 1.152 0.078 1.56e-02 4.11e+03 2.51e+01 bond pdb=" C GLN C 597 " pdb=" O GLN C 597 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.20e+01 bond pdb=" C GLN J 597 " pdb=" O GLN J 597 " ideal model delta sigma weight residual 1.237 1.197 0.039 1.17e-02 7.31e+03 1.13e+01 bond pdb=" N VAL C 187 " pdb=" CA VAL C 187 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.23e-02 6.61e+03 9.66e+00 bond pdb=" N VAL H 500 " pdb=" CA VAL H 500 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.26e-02 6.30e+03 8.57e+00 ... (remaining 37313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 49530 2.21 - 4.42: 795 4.42 - 6.63: 53 6.63 - 8.83: 6 8.83 - 11.04: 2 Bond angle restraints: 50386 Sorted by residual: angle pdb=" CA GLN J 597 " pdb=" C GLN J 597 " pdb=" O GLN J 597 " ideal model delta sigma weight residual 120.55 114.94 5.61 1.06e+00 8.90e-01 2.80e+01 angle pdb=" CA GLN C 597 " pdb=" C GLN C 597 " pdb=" O GLN C 597 " ideal model delta sigma weight residual 120.55 114.95 5.60 1.06e+00 8.90e-01 2.79e+01 angle pdb=" CA LYS C 196 " pdb=" C LYS C 196 " pdb=" O LYS C 196 " ideal model delta sigma weight residual 120.42 115.07 5.35 1.06e+00 8.90e-01 2.54e+01 angle pdb=" N VAL D 500 " pdb=" CA VAL D 500 " pdb=" C VAL D 500 " ideal model delta sigma weight residual 108.11 101.84 6.27 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA ARG D 499 " pdb=" C ARG D 499 " pdb=" O ARG D 499 " ideal model delta sigma weight residual 121.38 116.64 4.74 1.06e+00 8.90e-01 2.00e+01 ... (remaining 50381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 19939 17.82 - 35.64: 2021 35.64 - 53.45: 440 53.45 - 71.27: 98 71.27 - 89.09: 36 Dihedral angle restraints: 22534 sinusoidal: 9260 harmonic: 13274 Sorted by residual: dihedral pdb=" CA LYS H 650 " pdb=" C LYS H 650 " pdb=" N PHE H 651 " pdb=" CA PHE H 651 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA LYS D 650 " pdb=" C LYS D 650 " pdb=" N PHE D 651 " pdb=" CA PHE D 651 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA LYS C 493 " pdb=" C LYS C 493 " pdb=" N ILE C 494 " pdb=" CA ILE C 494 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 22531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4868 0.056 - 0.112: 709 0.112 - 0.167: 100 0.167 - 0.223: 11 0.223 - 0.279: 2 Chirality restraints: 5690 Sorted by residual: chirality pdb=" CA TYR C 109 " pdb=" N TYR C 109 " pdb=" C TYR C 109 " pdb=" CB TYR C 109 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA TYR J 109 " pdb=" N TYR J 109 " pdb=" C TYR J 109 " pdb=" CB TYR J 109 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ARG B 116 " pdb=" N ARG B 116 " pdb=" C ARG B 116 " pdb=" CB ARG B 116 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 5687 not shown) Planarity restraints: 6404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 716 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ASN J 716 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN J 716 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN J 717 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 315 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C LYS I 315 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS I 315 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS I 316 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS J 193 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.47e+00 pdb=" C HIS J 193 " -0.037 2.00e-02 2.50e+03 pdb=" O HIS J 193 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU J 194 " 0.012 2.00e-02 2.50e+03 ... (remaining 6401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1027 2.71 - 3.26: 38070 3.26 - 3.81: 58014 3.81 - 4.35: 70006 4.35 - 4.90: 122348 Nonbonded interactions: 289465 Sorted by model distance: nonbonded pdb=" O ASP C 669 " pdb=" OD1 ASP C 669 " model vdw 2.167 3.040 nonbonded pdb=" O ASP J 669 " pdb=" OD1 ASP J 669 " model vdw 2.168 3.040 nonbonded pdb=" O TYR G 285 " pdb=" OG SER G 286 " model vdw 2.210 3.040 nonbonded pdb=" O TYR B 285 " pdb=" OG SER B 286 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU G 143 " pdb=" OG1 THR G 144 " model vdw 2.228 3.040 ... (remaining 289460 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 425 or resid 440 through 467)) selection = (chain 'B' and (resid 3 through 39 or resid 73 through 120 or resid 131 through \ 209 or resid 212 through 243 or resid 262 through 338 or resid 340 through 467)) \ selection = (chain 'G' and (resid 3 through 39 or resid 73 through 120 or resid 131 through \ 209 or resid 212 through 243 or resid 262 through 338 or resid 340 through 467)) \ selection = (chain 'I' and (resid 3 through 425 or resid 440 through 467)) } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.090 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.004 0.078 37318 Z= 0.222 Angle : 0.648 11.042 50386 Z= 0.391 Chirality : 0.041 0.279 5690 Planarity : 0.004 0.060 6404 Dihedral : 15.368 89.091 13906 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.70 % Allowed : 13.09 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.13), residues: 4394 helix: 2.04 (0.10), residues: 2538 sheet: 0.51 (0.30), residues: 322 loop : -0.04 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 116 TYR 0.026 0.002 TYR A 188 PHE 0.016 0.001 PHE H 340 TRP 0.015 0.001 TRP C 623 HIS 0.013 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00380 (37318) covalent geometry : angle 0.64789 (50386) hydrogen bonds : bond 0.15689 ( 2078) hydrogen bonds : angle 5.84213 ( 6168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 810 time to evaluate : 1.494 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 288 MET cc_start: 0.8154 (tpt) cc_final: 0.7935 (mmt) REVERT: B 285 TYR cc_start: 0.8261 (m-80) cc_final: 0.8029 (m-10) REVERT: B 360 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7264 (mt-10) REVERT: C 60 SER cc_start: 0.8462 (t) cc_final: 0.8122 (p) REVERT: C 94 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7032 (mm-30) REVERT: C 626 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: D 406 GLU cc_start: 0.7715 (tp30) cc_final: 0.7461 (tp30) REVERT: E 249 ASN cc_start: 0.9023 (t0) cc_final: 0.8522 (t0) REVERT: E 262 GLN cc_start: 0.8320 (tp40) cc_final: 0.7625 (tm-30) REVERT: G 150 ASP cc_start: 0.8100 (m-30) cc_final: 0.7451 (m-30) REVERT: G 154 ASP cc_start: 0.7415 (m-30) cc_final: 0.7158 (m-30) REVERT: H 258 ILE cc_start: 0.8566 (tp) cc_final: 0.8163 (mt) REVERT: H 338 ASN cc_start: 0.7051 (p0) cc_final: 0.6770 (p0) REVERT: H 402 MET cc_start: 0.7273 (mtt) cc_final: 0.6772 (mtm) REVERT: I 320 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (m-40) REVERT: J 155 LYS cc_start: 0.8320 (tttt) cc_final: 0.8086 (ttmm) REVERT: J 438 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: J 727 LYS cc_start: 0.8377 (tptt) cc_final: 0.7355 (tttt) outliers start: 29 outliers final: 5 residues processed: 824 average time/residue: 0.2326 time to fit residues: 304.4139 Evaluate side-chains 484 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 476 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 TYR Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 320 ASN Chi-restraints excluded: chain J residue 438 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 316 HIS ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 GLN D 533 HIS D 535 GLN E 253 GLN G 161 ASN G 195 ASN G 294 ASN G 402 GLN H 136 GLN H 430 ASN H 532 GLN H 535 GLN I 23 GLN I 119 HIS I 294 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 624 GLN J 742 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.110022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.081981 restraints weight = 73780.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.083134 restraints weight = 44012.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.084186 restraints weight = 30130.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085704 restraints weight = 25610.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085709 restraints weight = 22054.010| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37318 Z= 0.145 Angle : 0.541 10.489 50386 Z= 0.285 Chirality : 0.040 0.243 5690 Planarity : 0.003 0.055 6404 Dihedral : 4.447 57.398 4831 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.36 % Allowed : 15.43 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.13), residues: 4394 helix: 2.41 (0.10), residues: 2606 sheet: 0.19 (0.29), residues: 330 loop : 0.11 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 371 TYR 0.022 0.001 TYR H 251 PHE 0.021 0.001 PHE H 193 TRP 0.014 0.001 TRP I 377 HIS 0.004 0.001 HIS G 119 Details of bonding type rmsd covalent geometry : bond 0.00329 (37318) covalent geometry : angle 0.54143 (50386) hydrogen bonds : bond 0.04965 ( 2078) hydrogen bonds : angle 4.28311 ( 6168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 533 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.8353 (mtp) cc_final: 0.8083 (ttm) REVERT: A 446 MET cc_start: 0.8136 (ptm) cc_final: 0.7754 (ptp) REVERT: B 27 THR cc_start: 0.8993 (m) cc_final: 0.8669 (p) REVERT: B 285 TYR cc_start: 0.8410 (m-80) cc_final: 0.8183 (m-10) REVERT: B 360 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7138 (mt-10) REVERT: C 60 SER cc_start: 0.8493 (t) cc_final: 0.8107 (p) REVERT: C 78 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7960 (tt) REVERT: D 558 GLU cc_start: 0.8338 (tp30) cc_final: 0.7955 (tm-30) REVERT: E 255 LYS cc_start: 0.8758 (tmtt) cc_final: 0.8497 (tptp) REVERT: E 262 GLN cc_start: 0.8230 (tp40) cc_final: 0.7610 (tm-30) REVERT: F 263 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7768 (tm-30) REVERT: G 146 LEU cc_start: 0.8981 (tp) cc_final: 0.8566 (tp) REVERT: G 150 ASP cc_start: 0.8202 (m-30) cc_final: 0.7503 (m-30) REVERT: G 154 ASP cc_start: 0.7559 (m-30) cc_final: 0.7191 (m-30) REVERT: G 157 ASP cc_start: 0.8064 (p0) cc_final: 0.7644 (m-30) REVERT: G 285 TYR cc_start: 0.8684 (m-80) cc_final: 0.8191 (m-80) REVERT: G 294 ASN cc_start: 0.9274 (t0) cc_final: 0.8769 (t0) REVERT: G 446 MET cc_start: 0.8993 (ptm) cc_final: 0.8643 (ptp) REVERT: H 191 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8345 (tp30) REVERT: H 406 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7218 (tm-30) REVERT: H 407 MET cc_start: 0.8589 (tmm) cc_final: 0.8358 (tmm) REVERT: H 562 GLU cc_start: 0.8279 (pp20) cc_final: 0.7893 (pt0) REVERT: H 745 LEU cc_start: 0.9535 (mt) cc_final: 0.9199 (tt) REVERT: I 327 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7453 (tp30) REVERT: I 446 MET cc_start: 0.9035 (ptm) cc_final: 0.8772 (ptp) REVERT: J 405 THR cc_start: 0.9080 (m) cc_final: 0.8733 (p) REVERT: J 431 MET cc_start: 0.8706 (tpp) cc_final: 0.8411 (tpp) REVERT: J 464 ASP cc_start: 0.8426 (t0) cc_final: 0.8211 (t70) REVERT: J 727 LYS cc_start: 0.8284 (tptt) cc_final: 0.7068 (tttt) REVERT: J 772 MET cc_start: 0.7745 (tpp) cc_final: 0.7411 (tpp) REVERT: J 787 LYS cc_start: 0.8824 (pttp) cc_final: 0.8571 (pttm) REVERT: K 239 ARG cc_start: 0.7115 (tpp-160) cc_final: 0.6605 (tpp-160) REVERT: K 242 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7623 (tm-30) outliers start: 98 outliers final: 54 residues processed: 602 average time/residue: 0.2116 time to fit residues: 213.0880 Evaluate side-chains 486 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 431 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 516 GLU Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 384 VAL Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 469 GLU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain K residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 2 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 359 optimal weight: 0.6980 chunk 297 optimal weight: 0.0670 chunk 316 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 418 optimal weight: 0.4980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 GLN B 316 HIS C 54 ASN ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN G 9 GLN G 190 HIS H 533 HIS ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 717 ASN J 756 ASN L 269 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.108784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.080310 restraints weight = 73987.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081991 restraints weight = 43500.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083046 restraints weight = 28850.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084390 restraints weight = 25025.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084397 restraints weight = 22001.056| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37318 Z= 0.147 Angle : 0.515 10.282 50386 Z= 0.267 Chirality : 0.040 0.189 5690 Planarity : 0.003 0.038 6404 Dihedral : 4.052 59.993 4820 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.92 % Allowed : 15.65 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.13), residues: 4394 helix: 2.59 (0.10), residues: 2610 sheet: 0.10 (0.29), residues: 340 loop : 0.06 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.018 0.001 TYR D 384 PHE 0.019 0.001 PHE H 490 TRP 0.010 0.001 TRP H 544 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00341 (37318) covalent geometry : angle 0.51520 (50386) hydrogen bonds : bond 0.04324 ( 2078) hydrogen bonds : angle 4.01647 ( 6168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 458 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8050 (m-30) cc_final: 0.7727 (m-30) REVERT: A 324 MET cc_start: 0.8537 (mtp) cc_final: 0.8286 (ttm) REVERT: A 399 GLU cc_start: 0.7560 (pt0) cc_final: 0.7242 (pm20) REVERT: A 424 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 446 MET cc_start: 0.8152 (ptm) cc_final: 0.7826 (ptp) REVERT: B 27 THR cc_start: 0.9056 (m) cc_final: 0.8752 (p) REVERT: B 325 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 360 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7123 (mt-10) REVERT: D 226 GLU cc_start: 0.7093 (tt0) cc_final: 0.6866 (tt0) REVERT: D 558 GLU cc_start: 0.8359 (tp30) cc_final: 0.7950 (tm-30) REVERT: E 255 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8458 (tptp) REVERT: E 262 GLN cc_start: 0.8205 (tp40) cc_final: 0.7711 (tm-30) REVERT: F 263 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7631 (tm-30) REVERT: G 150 ASP cc_start: 0.8261 (m-30) cc_final: 0.7690 (m-30) REVERT: G 154 ASP cc_start: 0.7605 (m-30) cc_final: 0.7197 (m-30) REVERT: G 157 ASP cc_start: 0.7995 (p0) cc_final: 0.7650 (m-30) REVERT: G 285 TYR cc_start: 0.8681 (m-80) cc_final: 0.8121 (m-80) REVERT: G 294 ASN cc_start: 0.9311 (t0) cc_final: 0.8640 (t0) REVERT: G 446 MET cc_start: 0.9090 (ptm) cc_final: 0.8704 (ptp) REVERT: H 191 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8341 (tp30) REVERT: H 230 ASN cc_start: 0.8814 (m-40) cc_final: 0.8556 (m110) REVERT: H 407 MET cc_start: 0.8626 (tmm) cc_final: 0.8401 (tmm) REVERT: H 497 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8100 (t0) REVERT: H 562 GLU cc_start: 0.8323 (pp20) cc_final: 0.7973 (pt0) REVERT: H 745 LEU cc_start: 0.9578 (mt) cc_final: 0.9352 (tt) REVERT: I 327 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7577 (tp30) REVERT: I 446 MET cc_start: 0.9024 (ptm) cc_final: 0.8766 (ptp) REVERT: J 72 LYS cc_start: 0.1665 (pttm) cc_final: 0.1033 (pttt) REVERT: J 86 ILE cc_start: 0.9121 (mp) cc_final: 0.8886 (tt) REVERT: J 405 THR cc_start: 0.9103 (m) cc_final: 0.8666 (p) REVERT: J 431 MET cc_start: 0.8762 (tpp) cc_final: 0.8459 (tpp) REVERT: J 727 LYS cc_start: 0.8264 (tptt) cc_final: 0.7034 (tttt) REVERT: J 772 MET cc_start: 0.7835 (tpp) cc_final: 0.7408 (tpp) REVERT: K 239 ARG cc_start: 0.7164 (tpp-160) cc_final: 0.6781 (tpp-160) REVERT: K 242 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7497 (tm-30) REVERT: L 241 GLU cc_start: 0.7955 (pm20) cc_final: 0.7582 (pm20) outliers start: 121 outliers final: 70 residues processed: 550 average time/residue: 0.1942 time to fit residues: 180.8684 Evaluate side-chains 468 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 395 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 497 ASP Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain L residue 243 LEU Chi-restraints excluded: chain L residue 249 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 338 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 347 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 313 optimal weight: 0.0020 chunk 278 optimal weight: 0.9980 chunk 233 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 HIS B 402 GLN ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN C 636 HIS C 718 ASN D 430 ASN G 133 ASN I 24 GLN I 397 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 GLN ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 244 ASN ** L 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081413 restraints weight = 73829.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083410 restraints weight = 42214.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084272 restraints weight = 27716.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085043 restraints weight = 24716.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085252 restraints weight = 22504.929| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37318 Z= 0.121 Angle : 0.493 12.086 50386 Z= 0.253 Chirality : 0.039 0.166 5690 Planarity : 0.003 0.039 6404 Dihedral : 3.843 58.494 4816 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.92 % Allowed : 16.80 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.13), residues: 4394 helix: 2.68 (0.10), residues: 2614 sheet: 0.15 (0.29), residues: 332 loop : 0.09 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 267 TYR 0.021 0.001 TYR I 188 PHE 0.044 0.001 PHE H 743 TRP 0.010 0.001 TRP C 354 HIS 0.005 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00278 (37318) covalent geometry : angle 0.49265 (50386) hydrogen bonds : bond 0.03926 ( 2078) hydrogen bonds : angle 3.88780 ( 6168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 456 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8013 (m-30) cc_final: 0.7691 (m-30) REVERT: A 327 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 397 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8530 (p0) REVERT: A 399 GLU cc_start: 0.7552 (pt0) cc_final: 0.7322 (pm20) REVERT: A 424 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8575 (tp) REVERT: A 446 MET cc_start: 0.8271 (ptm) cc_final: 0.7914 (ptp) REVERT: B 27 THR cc_start: 0.9038 (m) cc_final: 0.8734 (p) REVERT: B 130 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8144 (t0) REVERT: B 324 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7850 (tpp) REVERT: B 325 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8651 (mm) REVERT: B 360 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7116 (mt-10) REVERT: C 844 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8058 (mp) REVERT: E 255 LYS cc_start: 0.8757 (tmtt) cc_final: 0.8471 (tptp) REVERT: E 262 GLN cc_start: 0.8164 (tp40) cc_final: 0.7678 (tm-30) REVERT: F 263 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 150 ASP cc_start: 0.8288 (m-30) cc_final: 0.7705 (m-30) REVERT: G 154 ASP cc_start: 0.7605 (m-30) cc_final: 0.7191 (m-30) REVERT: G 157 ASP cc_start: 0.7882 (p0) cc_final: 0.7617 (m-30) REVERT: G 285 TYR cc_start: 0.8641 (m-80) cc_final: 0.8122 (m-80) REVERT: G 294 ASN cc_start: 0.9275 (t0) cc_final: 0.8580 (t0) REVERT: G 326 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8889 (mm) REVERT: H 230 ASN cc_start: 0.8835 (m-40) cc_final: 0.8620 (m110) REVERT: H 402 MET cc_start: 0.7887 (mmm) cc_final: 0.7673 (mmm) REVERT: H 407 MET cc_start: 0.8653 (tmm) cc_final: 0.8345 (tmm) REVERT: H 497 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8067 (t0) REVERT: H 562 GLU cc_start: 0.8379 (pp20) cc_final: 0.8001 (pt0) REVERT: H 745 LEU cc_start: 0.9592 (mt) cc_final: 0.9366 (tt) REVERT: I 187 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8164 (ptm160) REVERT: I 327 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7523 (tp30) REVERT: J 72 LYS cc_start: 0.1599 (pttm) cc_final: 0.1094 (pttt) REVERT: J 86 ILE cc_start: 0.9238 (mp) cc_final: 0.8974 (tt) REVERT: J 405 THR cc_start: 0.9119 (m) cc_final: 0.8700 (p) REVERT: J 431 MET cc_start: 0.8736 (tpp) cc_final: 0.8506 (tpp) REVERT: J 772 MET cc_start: 0.7902 (tpp) cc_final: 0.7397 (tpp) REVERT: J 787 LYS cc_start: 0.8877 (pttp) cc_final: 0.8616 (pttm) REVERT: K 242 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8181 (tm-30) REVERT: K 255 LYS cc_start: 0.8277 (ttmm) cc_final: 0.8069 (tttp) REVERT: K 262 GLN cc_start: 0.8602 (tp40) cc_final: 0.7909 (tm-30) outliers start: 121 outliers final: 72 residues processed: 550 average time/residue: 0.1944 time to fit residues: 179.0297 Evaluate side-chains 485 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 404 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 185 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 497 ASP Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain I residue 401 ILE Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain K residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 403 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 288 optimal weight: 0.0470 chunk 196 optimal weight: 0.9980 chunk 256 optimal weight: 0.0040 chunk 227 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 281 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 190 HIS B 316 HIS ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 ASN I 24 GLN I 397 ASN ** J 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 742 GLN L 262 GLN L 269 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.110842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082549 restraints weight = 73770.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084469 restraints weight = 42940.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085506 restraints weight = 28144.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.086181 restraints weight = 24591.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086326 restraints weight = 22471.914| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37318 Z= 0.105 Angle : 0.483 12.944 50386 Z= 0.247 Chirality : 0.038 0.193 5690 Planarity : 0.003 0.036 6404 Dihedral : 3.724 56.331 4816 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.80 % Allowed : 17.19 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.13), residues: 4394 helix: 2.81 (0.10), residues: 2604 sheet: 0.24 (0.29), residues: 332 loop : 0.07 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 267 TYR 0.017 0.001 TYR D 384 PHE 0.016 0.001 PHE B 311 TRP 0.009 0.001 TRP J 623 HIS 0.006 0.000 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00235 (37318) covalent geometry : angle 0.48263 (50386) hydrogen bonds : bond 0.03596 ( 2078) hydrogen bonds : angle 3.78177 ( 6168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 449 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7872 (m-30) cc_final: 0.7524 (m-30) REVERT: A 424 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 446 MET cc_start: 0.8248 (ptm) cc_final: 0.7895 (ptp) REVERT: B 9 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: B 27 THR cc_start: 0.9036 (m) cc_final: 0.8737 (p) REVERT: B 324 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (tpp) REVERT: B 325 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8690 (mm) REVERT: B 360 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7069 (mt-10) REVERT: C 844 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8026 (mp) REVERT: E 255 LYS cc_start: 0.8784 (tmtt) cc_final: 0.8462 (tptp) REVERT: E 262 GLN cc_start: 0.8158 (tp40) cc_final: 0.7688 (tm-30) REVERT: F 263 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7681 (tm-30) REVERT: G 150 ASP cc_start: 0.8407 (m-30) cc_final: 0.7717 (m-30) REVERT: G 154 ASP cc_start: 0.7572 (m-30) cc_final: 0.7131 (m-30) REVERT: G 157 ASP cc_start: 0.7777 (p0) cc_final: 0.7543 (m-30) REVERT: G 269 LEU cc_start: 0.8303 (mt) cc_final: 0.7904 (tp) REVERT: G 285 TYR cc_start: 0.8492 (m-80) cc_final: 0.7922 (m-80) REVERT: G 294 ASN cc_start: 0.9279 (t0) cc_final: 0.8535 (t0) REVERT: G 326 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8827 (mm) REVERT: H 230 ASN cc_start: 0.8846 (m-40) cc_final: 0.8618 (m-40) REVERT: H 407 MET cc_start: 0.8663 (tmm) cc_final: 0.8216 (tmm) REVERT: H 497 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8027 (t0) REVERT: H 562 GLU cc_start: 0.8345 (pp20) cc_final: 0.7995 (pt0) REVERT: H 745 LEU cc_start: 0.9588 (mt) cc_final: 0.9332 (pp) REVERT: I 327 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7455 (tp30) REVERT: I 377 TRP cc_start: 0.9046 (p-90) cc_final: 0.8758 (p-90) REVERT: I 446 MET cc_start: 0.9001 (ptm) cc_final: 0.8695 (ptm) REVERT: J 72 LYS cc_start: 0.1376 (pttm) cc_final: 0.0834 (pttt) REVERT: J 86 ILE cc_start: 0.9296 (mp) cc_final: 0.9044 (tt) REVERT: J 343 MET cc_start: 0.8091 (tmm) cc_final: 0.7846 (tpp) REVERT: J 431 MET cc_start: 0.8717 (tpp) cc_final: 0.8493 (tpp) REVERT: J 772 MET cc_start: 0.7861 (tpp) cc_final: 0.7414 (tpp) REVERT: J 787 LYS cc_start: 0.8893 (pttp) cc_final: 0.8576 (pttm) REVERT: K 242 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7921 (tm-30) REVERT: K 262 GLN cc_start: 0.8570 (tp40) cc_final: 0.7915 (tm-30) outliers start: 116 outliers final: 74 residues processed: 535 average time/residue: 0.2026 time to fit residues: 181.7131 Evaluate side-chains 482 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 401 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 304 LEU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 497 ASP Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 423 LEU Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 469 GLU Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain L residue 243 LEU Chi-restraints excluded: chain L residue 257 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 439 optimal weight: 0.9980 chunk 290 optimal weight: 0.5980 chunk 277 optimal weight: 3.9990 chunk 417 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 365 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 262 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN B 9 GLN B 316 HIS ** C 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN D 430 ASN H 414 GLN H 435 HIS I 76 HIS I 397 ASN J 54 ASN ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** 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 = 0.3527 r_free = 0.3527 target = 0.108886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080578 restraints weight = 73835.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.082308 restraints weight = 42316.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083198 restraints weight = 28612.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083853 restraints weight = 25152.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083956 restraints weight = 22940.172| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37318 Z= 0.139 Angle : 0.511 13.584 50386 Z= 0.261 Chirality : 0.039 0.171 5690 Planarity : 0.003 0.036 6404 Dihedral : 3.767 57.295 4816 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.84 % Allowed : 17.82 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.13), residues: 4394 helix: 2.77 (0.10), residues: 2610 sheet: 0.21 (0.29), residues: 338 loop : 0.04 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 267 TYR 0.024 0.001 TYR H 603 PHE 0.016 0.001 PHE F 260 TRP 0.010 0.001 TRP J 623 HIS 0.008 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00327 (37318) covalent geometry : angle 0.51080 (50386) hydrogen bonds : bond 0.03876 ( 2078) hydrogen bonds : angle 3.82404 ( 6168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 423 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7924 (m-30) cc_final: 0.7582 (m-30) REVERT: A 327 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: A 424 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8615 (tp) REVERT: A 446 MET cc_start: 0.8274 (ptm) cc_final: 0.7910 (ptp) REVERT: B 9 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: B 27 THR cc_start: 0.9058 (m) cc_final: 0.8753 (p) REVERT: B 130 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8145 (t0) REVERT: B 324 MET cc_start: 0.8106 (ttp) cc_final: 0.7813 (tpp) REVERT: B 325 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8701 (mm) REVERT: B 360 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7099 (mt-10) REVERT: C 844 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8087 (mp) REVERT: D 430 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7868 (m-40) REVERT: E 255 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8486 (tptp) REVERT: E 262 GLN cc_start: 0.8084 (tp40) cc_final: 0.7631 (tm-30) REVERT: F 263 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 150 ASP cc_start: 0.8387 (m-30) cc_final: 0.7671 (m-30) REVERT: G 154 ASP cc_start: 0.7623 (m-30) cc_final: 0.7175 (m-30) REVERT: G 157 ASP cc_start: 0.7832 (p0) cc_final: 0.7628 (m-30) REVERT: G 284 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7994 (mtm) REVERT: G 294 ASN cc_start: 0.9293 (t0) cc_final: 0.8861 (t0) REVERT: G 326 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8826 (mm) REVERT: H 180 ASP cc_start: 0.8295 (t0) cc_final: 0.8030 (t0) REVERT: H 407 MET cc_start: 0.8665 (tmm) cc_final: 0.8221 (tmm) REVERT: H 562 GLU cc_start: 0.8366 (pp20) cc_final: 0.7997 (pt0) REVERT: H 637 MET cc_start: 0.8528 (ptm) cc_final: 0.7994 (ppp) REVERT: H 648 LEU cc_start: 0.8643 (tp) cc_final: 0.8299 (pp) REVERT: H 745 LEU cc_start: 0.9600 (mt) cc_final: 0.9350 (pp) REVERT: I 327 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7526 (tp30) REVERT: I 446 MET cc_start: 0.9022 (ptm) cc_final: 0.8709 (ptm) REVERT: J 72 LYS cc_start: 0.1403 (pttm) cc_final: 0.0856 (pttt) REVERT: J 86 ILE cc_start: 0.9337 (mp) cc_final: 0.9096 (tt) REVERT: J 343 MET cc_start: 0.8073 (tmm) cc_final: 0.7832 (tpp) REVERT: J 431 MET cc_start: 0.8765 (tpp) cc_final: 0.8472 (tpp) REVERT: J 772 MET cc_start: 0.7961 (tpp) cc_final: 0.7474 (tpp) REVERT: J 787 LYS cc_start: 0.8894 (pttp) cc_final: 0.8609 (pttm) REVERT: K 242 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 255 LYS cc_start: 0.8434 (tttp) cc_final: 0.8010 (ttmm) REVERT: K 262 GLN cc_start: 0.8575 (tp40) cc_final: 0.7914 (tm-30) outliers start: 118 outliers final: 77 residues processed: 512 average time/residue: 0.1959 time to fit residues: 170.9569 Evaluate side-chains 483 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 397 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 ASN Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain I residue 423 LEU Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 391 CYS Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain J residue 847 ILE Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain L residue 243 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 373 optimal weight: 0.3980 chunk 347 optimal weight: 0.7980 chunk 280 optimal weight: 0.3980 chunk 226 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 317 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN B 316 HIS ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 742 GLN L 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080789 restraints weight = 73757.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083239 restraints weight = 43253.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083935 restraints weight = 27300.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084660 restraints weight = 24718.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084736 restraints weight = 22548.580| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37318 Z= 0.116 Angle : 0.498 14.346 50386 Z= 0.254 Chirality : 0.038 0.175 5690 Planarity : 0.003 0.037 6404 Dihedral : 3.716 56.759 4816 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.84 % Allowed : 17.50 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.13), residues: 4394 helix: 2.81 (0.10), residues: 2608 sheet: 0.45 (0.30), residues: 310 loop : 0.02 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 267 TYR 0.020 0.001 TYR H 603 PHE 0.019 0.001 PHE J 457 TRP 0.010 0.001 TRP J 623 HIS 0.007 0.001 HIS I 76 Details of bonding type rmsd covalent geometry : bond 0.00268 (37318) covalent geometry : angle 0.49841 (50386) hydrogen bonds : bond 0.03664 ( 2078) hydrogen bonds : angle 3.77371 ( 6168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 424 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7891 (m-30) cc_final: 0.7563 (m-30) REVERT: A 424 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 446 MET cc_start: 0.8290 (ptm) cc_final: 0.7909 (ptp) REVERT: B 27 THR cc_start: 0.9040 (m) cc_final: 0.8738 (p) REVERT: B 28 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7247 (mt-10) REVERT: B 324 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: B 325 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8721 (mm) REVERT: B 360 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7081 (mt-10) REVERT: B 462 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: C 844 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8053 (mp) REVERT: D 310 TYR cc_start: 0.8853 (m-10) cc_final: 0.8638 (m-10) REVERT: E 255 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8443 (tptp) REVERT: E 262 GLN cc_start: 0.8017 (tp40) cc_final: 0.7642 (tm-30) REVERT: F 245 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8400 (mttp) REVERT: F 263 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7666 (tm-30) REVERT: G 150 ASP cc_start: 0.8368 (m-30) cc_final: 0.7650 (m-30) REVERT: G 154 ASP cc_start: 0.7620 (m-30) cc_final: 0.7164 (m-30) REVERT: G 157 ASP cc_start: 0.7811 (p0) cc_final: 0.7606 (m-30) REVERT: G 284 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: G 294 ASN cc_start: 0.9296 (t0) cc_final: 0.8855 (t0) REVERT: G 324 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8432 (tpp) REVERT: G 326 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8832 (mm) REVERT: H 180 ASP cc_start: 0.8298 (t0) cc_final: 0.8010 (t0) REVERT: H 648 LEU cc_start: 0.8644 (tp) cc_final: 0.8278 (pp) REVERT: I 75 ASP cc_start: 0.8964 (p0) cc_final: 0.8748 (p0) REVERT: I 327 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7454 (tp30) REVERT: I 446 MET cc_start: 0.9050 (ptm) cc_final: 0.8738 (ptm) REVERT: J 72 LYS cc_start: 0.1370 (pttm) cc_final: 0.0824 (pttt) REVERT: J 86 ILE cc_start: 0.9337 (mp) cc_final: 0.9112 (tt) REVERT: J 343 MET cc_start: 0.8077 (tmm) cc_final: 0.7847 (tpp) REVERT: J 431 MET cc_start: 0.8753 (tpp) cc_final: 0.8497 (tpp) REVERT: J 772 MET cc_start: 0.7961 (tpp) cc_final: 0.7464 (tpp) REVERT: J 787 LYS cc_start: 0.8905 (pttp) cc_final: 0.8609 (pttm) REVERT: K 242 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8044 (tm-30) REVERT: K 262 GLN cc_start: 0.8571 (tp40) cc_final: 0.7945 (tm-30) REVERT: L 240 GLU cc_start: 0.7678 (pp20) cc_final: 0.7077 (pp20) outliers start: 118 outliers final: 91 residues processed: 512 average time/residue: 0.2022 time to fit residues: 176.6819 Evaluate side-chains 498 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 399 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 324 MET Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain G residue 445 GLU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain I residue 423 LEU Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain J residue 847 ILE Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain L residue 257 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 111 optimal weight: 0.9980 chunk 381 optimal weight: 0.8980 chunk 271 optimal weight: 0.5980 chunk 391 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 265 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 222 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 442 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 316 HIS ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.108988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080100 restraints weight = 73236.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082493 restraints weight = 43105.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083371 restraints weight = 27387.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084658 restraints weight = 25414.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084831 restraints weight = 22212.865| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37318 Z= 0.133 Angle : 0.516 14.338 50386 Z= 0.261 Chirality : 0.039 0.201 5690 Planarity : 0.003 0.041 6404 Dihedral : 3.752 57.174 4816 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.94 % Allowed : 17.67 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.13), residues: 4394 helix: 2.81 (0.10), residues: 2608 sheet: 0.18 (0.29), residues: 334 loop : 0.02 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 267 TYR 0.019 0.001 TYR H 603 PHE 0.017 0.001 PHE F 260 TRP 0.010 0.001 TRP J 623 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00313 (37318) covalent geometry : angle 0.51602 (50386) hydrogen bonds : bond 0.03781 ( 2078) hydrogen bonds : angle 3.78222 ( 6168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 406 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7920 (m-30) cc_final: 0.7605 (m-30) REVERT: A 327 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: A 424 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8626 (tp) REVERT: A 446 MET cc_start: 0.8300 (ptm) cc_final: 0.7908 (ptp) REVERT: B 27 THR cc_start: 0.9055 (m) cc_final: 0.8754 (p) REVERT: B 28 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7272 (mt-10) REVERT: B 325 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8724 (mm) REVERT: B 360 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7075 (mt-10) REVERT: C 745 GLN cc_start: 0.8003 (tp40) cc_final: 0.7272 (tp40) REVERT: C 844 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 555 TRP cc_start: 0.8748 (m-10) cc_final: 0.8506 (m-10) REVERT: E 255 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8478 (tptp) REVERT: E 262 GLN cc_start: 0.8025 (tp40) cc_final: 0.7651 (tm-30) REVERT: F 245 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8406 (mttp) REVERT: F 263 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7696 (tm-30) REVERT: G 150 ASP cc_start: 0.8381 (m-30) cc_final: 0.7665 (m-30) REVERT: G 154 ASP cc_start: 0.7624 (m-30) cc_final: 0.7175 (m-30) REVERT: G 294 ASN cc_start: 0.9307 (t0) cc_final: 0.8870 (t0) REVERT: G 324 MET cc_start: 0.8642 (tpp) cc_final: 0.8421 (tpp) REVERT: G 326 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8839 (mm) REVERT: H 180 ASP cc_start: 0.8319 (t0) cc_final: 0.8040 (t0) REVERT: H 637 MET cc_start: 0.8471 (ptm) cc_final: 0.7968 (ppp) REVERT: H 648 LEU cc_start: 0.8636 (tp) cc_final: 0.8251 (pp) REVERT: H 721 LEU cc_start: 0.8977 (mm) cc_final: 0.8758 (pp) REVERT: H 745 LEU cc_start: 0.9209 (tt) cc_final: 0.8750 (mt) REVERT: I 75 ASP cc_start: 0.8854 (p0) cc_final: 0.8626 (p0) REVERT: I 234 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7244 (m170) REVERT: I 327 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7535 (tp30) REVERT: I 446 MET cc_start: 0.9058 (ptm) cc_final: 0.8741 (ptm) REVERT: J 72 LYS cc_start: 0.1431 (pttm) cc_final: 0.0881 (pttt) REVERT: J 86 ILE cc_start: 0.9360 (mp) cc_final: 0.9144 (tt) REVERT: J 343 MET cc_start: 0.8066 (tmm) cc_final: 0.7864 (tpp) REVERT: J 431 MET cc_start: 0.8749 (tpp) cc_final: 0.8465 (tpp) REVERT: J 483 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: J 529 MET cc_start: 0.5960 (tmm) cc_final: 0.5438 (tmm) REVERT: J 772 MET cc_start: 0.7959 (tpp) cc_final: 0.7496 (tpp) REVERT: J 787 LYS cc_start: 0.8891 (pttp) cc_final: 0.8590 (pttm) REVERT: J 831 MET cc_start: 0.8613 (ppp) cc_final: 0.8310 (ppp) REVERT: K 242 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8054 (tm-30) REVERT: K 262 GLN cc_start: 0.8585 (tp40) cc_final: 0.7965 (tm-30) REVERT: L 240 GLU cc_start: 0.7693 (pp20) cc_final: 0.7015 (pp20) outliers start: 122 outliers final: 91 residues processed: 497 average time/residue: 0.1953 time to fit residues: 166.3447 Evaluate side-chains 485 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 387 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain I residue 423 LEU Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 483 GLN Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain J residue 847 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 214 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 429 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 357 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 386 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 133 ASN B 316 HIS ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 742 GLN L 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079946 restraints weight = 73563.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082294 restraints weight = 42880.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083009 restraints weight = 27481.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083587 restraints weight = 25918.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.083758 restraints weight = 23104.768| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37318 Z= 0.136 Angle : 0.526 14.590 50386 Z= 0.265 Chirality : 0.039 0.172 5690 Planarity : 0.003 0.046 6404 Dihedral : 3.763 57.413 4816 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.77 % Allowed : 18.13 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.13), residues: 4394 helix: 2.78 (0.10), residues: 2612 sheet: -0.01 (0.29), residues: 354 loop : 0.02 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 267 TYR 0.018 0.001 TYR D 384 PHE 0.017 0.001 PHE F 260 TRP 0.011 0.001 TRP J 623 HIS 0.010 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00320 (37318) covalent geometry : angle 0.52634 (50386) hydrogen bonds : bond 0.03820 ( 2078) hydrogen bonds : angle 3.79807 ( 6168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 407 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8310 (mmm) cc_final: 0.7861 (ttp) REVERT: A 228 ASP cc_start: 0.7931 (m-30) cc_final: 0.7621 (m-30) REVERT: A 327 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 424 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 446 MET cc_start: 0.8321 (ptm) cc_final: 0.7918 (ptp) REVERT: B 27 THR cc_start: 0.9054 (m) cc_final: 0.8751 (p) REVERT: B 325 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 360 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7061 (mt-10) REVERT: C 483 GLN cc_start: 0.8037 (mp10) cc_final: 0.7749 (mp10) REVERT: C 745 GLN cc_start: 0.7993 (tp40) cc_final: 0.7264 (tp40) REVERT: C 844 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8113 (mp) REVERT: E 255 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8470 (tptp) REVERT: E 262 GLN cc_start: 0.8042 (tp40) cc_final: 0.7656 (tm-30) REVERT: F 245 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8420 (mttp) REVERT: F 263 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7629 (tm-30) REVERT: G 150 ASP cc_start: 0.8400 (m-30) cc_final: 0.7677 (m-30) REVERT: G 154 ASP cc_start: 0.7632 (m-30) cc_final: 0.7185 (m-30) REVERT: G 294 ASN cc_start: 0.9304 (t0) cc_final: 0.8857 (t0) REVERT: G 326 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8834 (mm) REVERT: H 180 ASP cc_start: 0.8399 (t0) cc_final: 0.8123 (t0) REVERT: H 636 PHE cc_start: 0.8883 (p90) cc_final: 0.6947 (m-10) REVERT: H 637 MET cc_start: 0.8399 (ptm) cc_final: 0.7466 (ppp) REVERT: H 648 LEU cc_start: 0.8619 (tp) cc_final: 0.8206 (pp) REVERT: H 745 LEU cc_start: 0.9192 (tt) cc_final: 0.8752 (mt) REVERT: I 75 ASP cc_start: 0.8885 (p0) cc_final: 0.8596 (p0) REVERT: I 234 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7273 (m170) REVERT: I 327 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7566 (tp30) REVERT: I 446 MET cc_start: 0.9066 (ptm) cc_final: 0.8760 (ptm) REVERT: J 72 LYS cc_start: 0.1339 (pttm) cc_final: 0.0704 (pttt) REVERT: J 86 ILE cc_start: 0.9372 (mp) cc_final: 0.9161 (tt) REVERT: J 431 MET cc_start: 0.8764 (tpp) cc_final: 0.8466 (tpp) REVERT: J 772 MET cc_start: 0.8026 (tpp) cc_final: 0.7531 (tpp) REVERT: J 787 LYS cc_start: 0.8901 (pttp) cc_final: 0.8596 (pttm) REVERT: J 831 MET cc_start: 0.8652 (ppp) cc_final: 0.8296 (ppp) REVERT: K 242 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8071 (tm-30) REVERT: K 262 GLN cc_start: 0.8579 (tp40) cc_final: 0.7976 (tm-30) REVERT: L 240 GLU cc_start: 0.7710 (pp20) cc_final: 0.6990 (pp20) outliers start: 115 outliers final: 95 residues processed: 494 average time/residue: 0.1986 time to fit residues: 167.0160 Evaluate side-chains 498 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 397 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 423 LEU Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 391 CYS Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 786 VAL Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain J residue 847 ILE Chi-restraints excluded: chain K residue 261 LEU Chi-restraints excluded: chain L residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 336 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 364 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 316 HIS ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 397 ASN ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.109175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.080694 restraints weight = 73425.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082784 restraints weight = 42339.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.083758 restraints weight = 27839.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084418 restraints weight = 24413.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.084570 restraints weight = 22394.990| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37318 Z= 0.127 Angle : 0.532 15.974 50386 Z= 0.265 Chirality : 0.039 0.219 5690 Planarity : 0.003 0.050 6404 Dihedral : 3.741 56.842 4816 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.53 % Allowed : 18.49 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.13), residues: 4394 helix: 2.81 (0.10), residues: 2606 sheet: 0.20 (0.29), residues: 334 loop : 0.04 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 267 TYR 0.019 0.001 TYR H 384 PHE 0.017 0.001 PHE F 260 TRP 0.010 0.001 TRP D 544 HIS 0.008 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00297 (37318) covalent geometry : angle 0.53170 (50386) hydrogen bonds : bond 0.03704 ( 2078) hydrogen bonds : angle 3.76650 ( 6168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8788 Ramachandran restraints generated. 4394 Oldfield, 0 Emsley, 4394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 407 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8250 (mmm) cc_final: 0.7761 (mpp) REVERT: A 228 ASP cc_start: 0.7907 (m-30) cc_final: 0.7604 (m-30) REVERT: A 327 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: A 424 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 446 MET cc_start: 0.8303 (ptm) cc_final: 0.7909 (ptp) REVERT: B 27 THR cc_start: 0.9027 (m) cc_final: 0.8738 (p) REVERT: B 360 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7076 (mt-10) REVERT: C 483 GLN cc_start: 0.8059 (mp10) cc_final: 0.7734 (mp10) REVERT: C 844 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8081 (mp) REVERT: E 255 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8484 (tptp) REVERT: E 262 GLN cc_start: 0.8026 (tp40) cc_final: 0.7543 (tm-30) REVERT: E 266 ASP cc_start: 0.7800 (p0) cc_final: 0.7297 (p0) REVERT: F 245 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8558 (mttp) REVERT: F 263 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7644 (tm-30) REVERT: G 150 ASP cc_start: 0.8408 (m-30) cc_final: 0.7671 (m-30) REVERT: G 154 ASP cc_start: 0.7629 (m-30) cc_final: 0.7169 (m-30) REVERT: G 294 ASN cc_start: 0.9297 (t0) cc_final: 0.8854 (t0) REVERT: G 325 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8931 (mm) REVERT: G 326 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8787 (mm) REVERT: H 180 ASP cc_start: 0.8387 (t0) cc_final: 0.8119 (t0) REVERT: H 636 PHE cc_start: 0.8860 (p90) cc_final: 0.6895 (m-10) REVERT: H 637 MET cc_start: 0.8374 (ptm) cc_final: 0.7539 (ppp) REVERT: H 648 LEU cc_start: 0.8581 (tp) cc_final: 0.8174 (pp) REVERT: H 745 LEU cc_start: 0.9167 (tt) cc_final: 0.8707 (mt) REVERT: I 75 ASP cc_start: 0.8923 (p0) cc_final: 0.8694 (p0) REVERT: I 234 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7258 (m170) REVERT: I 327 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7548 (tp30) REVERT: I 446 MET cc_start: 0.9058 (ptm) cc_final: 0.8742 (ptm) REVERT: J 72 LYS cc_start: 0.1403 (pttm) cc_final: 0.0750 (pttt) REVERT: J 431 MET cc_start: 0.8745 (tpp) cc_final: 0.8457 (tpp) REVERT: J 772 MET cc_start: 0.7959 (tpp) cc_final: 0.7495 (tpp) REVERT: J 787 LYS cc_start: 0.8887 (pttp) cc_final: 0.8586 (pttm) REVERT: J 831 MET cc_start: 0.8588 (ppp) cc_final: 0.8273 (ppp) REVERT: K 242 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8044 (tm-30) REVERT: K 262 GLN cc_start: 0.8580 (tp40) cc_final: 0.7992 (tm-30) REVERT: L 240 GLU cc_start: 0.7660 (pp20) cc_final: 0.7015 (pp20) outliers start: 105 outliers final: 90 residues processed: 487 average time/residue: 0.2140 time to fit residues: 177.8437 Evaluate side-chains 490 residues out of total 4216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 394 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 CYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 447 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 586 LEU Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 725 VAL Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain E residue 253 GLN Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 325 LEU Chi-restraints excluded: chain G residue 326 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 404 THR Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain H residue 141 TYR Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 317 ILE Chi-restraints excluded: chain H residue 419 LEU Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 234 HIS Chi-restraints excluded: chain I residue 266 LEU Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 397 ASN Chi-restraints excluded: chain I residue 464 CYS Chi-restraints excluded: chain J residue 61 CYS Chi-restraints excluded: chain J residue 188 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 306 ILE Chi-restraints excluded: chain J residue 324 ILE Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 379 LEU Chi-restraints excluded: chain J residue 385 LEU Chi-restraints excluded: chain J residue 391 CYS Chi-restraints excluded: chain J residue 406 THR Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 464 ASP Chi-restraints excluded: chain J residue 580 VAL Chi-restraints excluded: chain J residue 616 SER Chi-restraints excluded: chain J residue 648 CYS Chi-restraints excluded: chain J residue 659 ILE Chi-restraints excluded: chain J residue 786 VAL Chi-restraints excluded: chain J residue 790 LEU Chi-restraints excluded: chain J residue 847 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 159 optimal weight: 0.0980 chunk 186 optimal weight: 0.0070 chunk 226 optimal weight: 0.0010 chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 201 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 442 optimal weight: 0.7980 chunk 417 optimal weight: 2.9990 chunk 307 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 overall best weight: 0.2404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 316 HIS ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 ASN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080609 restraints weight = 73206.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.082751 restraints weight = 42923.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.083648 restraints weight = 27986.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084363 restraints weight = 24880.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084460 restraints weight = 22958.144| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.302 37318 Z= 0.155 Angle : 0.637 59.198 50386 Z= 0.344 Chirality : 0.041 1.143 5690 Planarity : 0.003 0.072 6404 Dihedral : 3.766 56.875 4816 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 18.80 % Favored : 78.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.13), residues: 4394 helix: 2.83 (0.10), residues: 2606 sheet: 0.20 (0.29), residues: 334 loop : 0.05 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 267 TYR 0.070 0.001 TYR G 318 PHE 0.013 0.001 PHE H 490 TRP 0.010 0.001 TRP J 623 HIS 0.007 0.001 HIS I 76 Details of bonding type rmsd covalent geometry : bond 0.00351 (37318) covalent geometry : angle 0.63731 (50386) hydrogen bonds : bond 0.03672 ( 2078) hydrogen bonds : angle 3.77280 ( 6168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6292.25 seconds wall clock time: 109 minutes 50.83 seconds (6590.83 seconds total)