Starting phenix.real_space_refine on Fri Jun 13 13:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.map" model { file = "/net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or4_17117/06_2025/8or4_17117.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 85 5.16 5 C 9526 2.51 5 N 2557 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5231 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 11, 'TRANS': 644} Chain breaks: 7 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 9, 'PHE:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 311 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 6347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6347 Classifications: {'peptide': 843} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 37, 'TRANS': 805} Chain breaks: 11 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 7, 'ASP:plan': 4, 'PHE:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 127 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 984 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1616 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 5 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 303 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 153 Chain: "H" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 244 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 111 Time building chain proxies: 8.68, per 1000 atoms: 0.58 Number of scatterers: 15036 At special positions: 0 Unit cell: (126.36, 179.28, 153.36, 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 85 16.00 O 2868 8.00 N 2557 7.00 C 9526 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: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 4 sheets defined 66.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.529A pdb=" N GLY A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.965A pdb=" N HIS A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 107 removed outlier: 3.636A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 3.853A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.540A pdb=" N ASP A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.993A pdb=" N GLN A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 225 through 255 removed outlier: 5.382A pdb=" N SER A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.953A pdb=" N MET A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN A 276 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 296 removed outlier: 3.727A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.091A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 332 through 356 removed outlier: 4.607A pdb=" N LEU A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.762A pdb=" N LEU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.833A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.666A pdb=" N MET A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.584A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 423 " --> pdb=" O PRO A 419 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.941A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.888A pdb=" N HIS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 Processing helix chain 'A' and resid 497 through 528 removed outlier: 3.862A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 4.003A pdb=" N ARG A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N SER A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.695A pdb=" N LEU A 612 " --> pdb=" O MET A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 630 removed outlier: 4.098A pdb=" N ASP A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 628 " --> pdb=" O GLN A 624 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 3.523A pdb=" N SER A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 722 removed outlier: 3.864A pdb=" N GLN A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.699A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.864A pdb=" N THR B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 16 removed outlier: 4.166A pdb=" N LEU C 11 " --> pdb=" O HIS C 7 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 36 removed outlier: 3.738A pdb=" N ARG C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.940A pdb=" N GLN C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.908A pdb=" N MET C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.563A pdb=" N SER C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 Processing helix chain 'C' and resid 140 through 143 Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.848A pdb=" N LEU C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.546A pdb=" N VAL C 170 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN C 171 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.889A pdb=" N ILE C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 4.147A pdb=" N THR C 185 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.698A pdb=" N CYS C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.930A pdb=" N GLU C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.649A pdb=" N SER C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 removed outlier: 4.169A pdb=" N GLU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.144A pdb=" N ASN C 265 " --> pdb=" O VAL C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.702A pdb=" N CYS C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 303 removed outlier: 4.302A pdb=" N LYS C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 4.021A pdb=" N ARG C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.765A pdb=" N ALA C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.903A pdb=" N ALA C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.374A pdb=" N MET C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Proline residue: C 433 - end of helix removed outlier: 3.913A pdb=" N LYS C 441 " --> pdb=" O LYS C 437 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET C 443 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 465 removed outlier: 4.044A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 removed outlier: 4.026A pdb=" N ASN C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 516 through 528 Proline residue: C 522 - end of helix Processing helix chain 'C' and resid 532 through 549 removed outlier: 3.705A pdb=" N THR C 536 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU C 541 " --> pdb=" O SER C 537 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 577 removed outlier: 4.280A pdb=" N LYS C 566 " --> pdb=" O THR C 562 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP C 567 " --> pdb=" O PRO C 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.538A pdb=" N GLY C 605 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER C 606 " --> pdb=" O ASN C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'C' and resid 607 through 621 removed outlier: 3.830A pdb=" N LYS C 620 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 644 through 650 Processing helix chain 'C' and resid 651 through 657 Processing helix chain 'C' and resid 666 through 677 removed outlier: 3.878A pdb=" N LEU C 671 " --> pdb=" O LYS C 667 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.633A pdb=" N ALA C 687 " --> pdb=" O SER C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.899A pdb=" N ASP C 695 " --> pdb=" O ASP C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 Proline residue: C 699 - end of helix No H-bonds generated for 'chain 'C' and resid 696 through 701' Processing helix chain 'C' and resid 702 through 720 removed outlier: 4.428A pdb=" N VAL C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 711 " --> pdb=" O HIS C 707 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 718 " --> pdb=" O SER C 714 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 719 " --> pdb=" O PHE C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 743 Processing helix chain 'C' and resid 758 through 762 Processing helix chain 'C' and resid 763 through 768 Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.591A pdb=" N SER C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU C 806 " --> pdb=" O CYS C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 827 through 836 removed outlier: 3.610A pdb=" N THR C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 877 removed outlier: 4.280A pdb=" N ALA C 876 " --> pdb=" O VAL C 872 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.667A pdb=" N ASN C 887 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 917 removed outlier: 3.836A pdb=" N LYS C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 933 removed outlier: 4.148A pdb=" N ILE C 932 " --> pdb=" O TYR C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 953 Processing helix chain 'D' and resid 20 through 23 Processing helix chain 'D' and resid 24 through 33 removed outlier: 4.501A pdb=" N MET D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 31 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.016A pdb=" N HIS D 65 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS D 66 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 67 " --> pdb=" O HIS D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.949A pdb=" N GLN D 96 " --> pdb=" O PRO D 92 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 98 " --> pdb=" O TRP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.928A pdb=" N GLU D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASN D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 137 through 144 removed outlier: 4.748A pdb=" N ARG D 142 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.851A pdb=" N LEU E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 132 removed outlier: 3.674A pdb=" N ARG E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 159 removed outlier: 3.576A pdb=" N THR E 152 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 Processing helix chain 'E' and resid 219 through 229 removed outlier: 4.077A pdb=" N ILE E 222 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN E 224 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 226 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS E 228 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.816A pdb=" N LYS G 30 " --> pdb=" O LYS G 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 208 through 218 removed outlier: 4.064A pdb=" N ARG H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE H 215 " --> pdb=" O GLN H 211 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 539 removed outlier: 6.299A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.650A pdb=" N ILE D 4 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 16 " --> pdb=" O ILE D 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'E' and resid 185 through 189 removed outlier: 3.570A pdb=" N SER E 212 " --> pdb=" O MET E 186 " (cutoff:3.500A) 729 hydrogen bonds defined for protein. 2121 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: 4.00 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2721 1.33 - 1.45: 3439 1.45 - 1.57: 8954 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 15236 Sorted by residual: bond pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.45e+01 bond pdb=" N GLN C 854 " pdb=" CA GLN C 854 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.20e-02 6.94e+03 1.24e+01 bond pdb=" C GLN C 854 " pdb=" O GLN C 854 " ideal model delta sigma weight residual 1.236 1.202 0.035 1.15e-02 7.56e+03 9.02e+00 bond pdb=" CA GLN C 854 " pdb=" CB GLN C 854 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.56e-02 4.11e+03 5.50e+00 bond pdb=" N GLU C 856 " pdb=" CA GLU C 856 " ideal model delta sigma weight residual 1.456 1.428 0.027 1.26e-02 6.30e+03 4.62e+00 ... (remaining 15231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 20286 1.93 - 3.86: 304 3.86 - 5.78: 35 5.78 - 7.71: 10 7.71 - 9.64: 4 Bond angle restraints: 20639 Sorted by residual: angle pdb=" N GLN C 854 " pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 111.11 117.41 -6.30 1.20e+00 6.94e-01 2.76e+01 angle pdb=" CA ARG E 415 " pdb=" CB ARG E 415 " pdb=" CG ARG E 415 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.65 103.74 6.91 1.58e+00 4.01e-01 1.91e+01 angle pdb=" N GLU C 856 " pdb=" CA GLU C 856 " pdb=" CB GLU C 856 " ideal model delta sigma weight residual 110.56 104.44 6.12 1.46e+00 4.69e-01 1.76e+01 angle pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta sigma weight residual 110.74 104.38 6.36 1.61e+00 3.86e-01 1.56e+01 ... (remaining 20634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8157 17.91 - 35.81: 906 35.81 - 53.72: 229 53.72 - 71.63: 37 71.63 - 89.53: 14 Dihedral angle restraints: 9343 sinusoidal: 3508 harmonic: 5835 Sorted by residual: dihedral pdb=" CA ARG C 664 " pdb=" C ARG C 664 " pdb=" N ALA C 665 " pdb=" CA ALA C 665 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU C 925 " pdb=" C LEU C 925 " pdb=" N LYS C 926 " pdb=" CA LYS C 926 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" N SER C 852 " pdb=" C SER C 852 " pdb=" CA SER C 852 " pdb=" CB SER C 852 " ideal model delta harmonic sigma weight residual 122.80 112.77 10.03 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 9340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2364 0.071 - 0.143: 143 0.143 - 0.214: 0 0.214 - 0.285: 1 0.285 - 0.357: 4 Chirality restraints: 2512 Sorted by residual: chirality pdb=" CA ARG A 561 " pdb=" N ARG A 561 " pdb=" C ARG A 561 " pdb=" CB ARG A 561 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA ARG E 294 " pdb=" N ARG E 294 " pdb=" C ARG E 294 " pdb=" CB ARG E 294 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLN C 854 " pdb=" N GLN C 854 " pdb=" C GLN C 854 " pdb=" CB GLN C 854 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2509 not shown) Planarity restraints: 2611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 625 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ARG C 625 " -0.075 2.00e-02 2.50e+03 pdb=" O ARG C 625 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU C 626 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 698 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO C 699 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 853 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C GLY C 853 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY C 853 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN C 854 " 0.014 2.00e-02 2.50e+03 ... (remaining 2608 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 122 2.52 - 3.12: 12505 3.12 - 3.71: 22644 3.71 - 4.31: 28014 4.31 - 4.90: 46238 Nonbonded interactions: 109523 Sorted by model distance: nonbonded pdb=" O LYS C 914 " pdb=" OG SER C 918 " model vdw 1.930 3.040 nonbonded pdb=" OH TYR C 372 " pdb=" OG1 THR C 405 " model vdw 1.994 3.040 nonbonded pdb=" OD2 ASP A 427 " pdb=" CG MET A 469 " model vdw 2.012 3.440 nonbonded pdb=" NZ LYS C 667 " pdb=" OD1 ASP C 705 " model vdw 2.017 3.120 nonbonded pdb=" O PHE C 371 " pdb=" OG1 THR C 374 " model vdw 2.019 3.040 ... (remaining 109518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15236 Z= 0.131 Angle : 0.588 9.639 20639 Z= 0.307 Chirality : 0.037 0.357 2512 Planarity : 0.004 0.072 2611 Dihedral : 16.205 89.532 5503 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.31 % Allowed : 24.89 % Favored : 74.80 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1914 helix: 1.35 (0.17), residues: 1026 sheet: 0.42 (1.35), residues: 21 loop : -1.68 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.002 0.000 HIS A 343 PHE 0.020 0.001 PHE A 402 TYR 0.012 0.001 TYR A 99 ARG 0.007 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.15278 ( 729) hydrogen bonds : angle 5.86386 ( 2121) covalent geometry : bond 0.00265 (15236) covalent geometry : angle 0.58847 (20639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 355 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8648 (tttt) cc_final: 0.7986 (tptp) REVERT: A 139 TYR cc_start: 0.7543 (t80) cc_final: 0.7310 (t80) REVERT: A 196 ILE cc_start: 0.7739 (mt) cc_final: 0.7328 (mm) REVERT: A 242 ARG cc_start: 0.7568 (ptt90) cc_final: 0.7322 (ptt90) REVERT: A 271 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 315 LYS cc_start: 0.6995 (mmtm) cc_final: 0.6676 (mmmm) REVERT: A 377 TYR cc_start: 0.8109 (m-80) cc_final: 0.7563 (m-80) REVERT: A 451 VAL cc_start: 0.7904 (t) cc_final: 0.7644 (t) REVERT: A 501 THR cc_start: 0.6782 (m) cc_final: 0.5522 (t) REVERT: A 509 GLN cc_start: 0.6005 (tp-100) cc_final: 0.5745 (tp-100) REVERT: A 627 ASP cc_start: 0.7569 (m-30) cc_final: 0.7228 (m-30) REVERT: C 25 MET cc_start: 0.7169 (mmm) cc_final: 0.6659 (mmm) REVERT: C 63 GLU cc_start: 0.8535 (tt0) cc_final: 0.7720 (tp30) REVERT: C 158 MET cc_start: 0.7309 (ttp) cc_final: 0.6976 (ttp) REVERT: C 234 TYR cc_start: 0.6864 (m-80) cc_final: 0.6475 (m-80) REVERT: C 451 ARG cc_start: 0.7535 (mtt180) cc_final: 0.7127 (mtt180) REVERT: C 593 MET cc_start: 0.8058 (tpp) cc_final: 0.7568 (tpp) REVERT: C 679 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7962 (ttmt) REVERT: C 793 LYS cc_start: 0.7957 (mttp) cc_final: 0.7733 (mttm) outliers start: 5 outliers final: 2 residues processed: 359 average time/residue: 0.2626 time to fit residues: 139.5679 Evaluate side-chains 335 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 851 LEU Chi-restraints excluded: chain E residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 0.0370 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS A 700 HIS C 299 ASN C 514 HIS C 887 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.158877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135249 restraints weight = 30860.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.139419 restraints weight = 17152.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.142209 restraints weight = 10844.139| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15236 Z= 0.145 Angle : 0.668 10.559 20639 Z= 0.335 Chirality : 0.041 0.202 2512 Planarity : 0.004 0.064 2611 Dihedral : 4.332 27.274 2061 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.18 % Allowed : 22.08 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1914 helix: 1.15 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 410 HIS 0.005 0.001 HIS C 173 PHE 0.026 0.002 PHE A 498 TYR 0.015 0.001 TYR A 278 ARG 0.008 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 729) hydrogen bonds : angle 4.63368 ( 2121) covalent geometry : bond 0.00318 (15236) covalent geometry : angle 0.66847 (20639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 370 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7264 (tp) cc_final: 0.6441 (tp) REVERT: A 117 LYS cc_start: 0.8609 (tttt) cc_final: 0.7982 (tptp) REVERT: A 123 TRP cc_start: 0.7166 (t60) cc_final: 0.6795 (t60) REVERT: A 271 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 315 LYS cc_start: 0.7293 (mmtm) cc_final: 0.7002 (mmtp) REVERT: A 331 ASP cc_start: 0.7189 (t0) cc_final: 0.6880 (t0) REVERT: A 451 VAL cc_start: 0.8135 (t) cc_final: 0.7919 (t) REVERT: A 469 MET cc_start: 0.6754 (tpp) cc_final: 0.6477 (tpp) REVERT: A 501 THR cc_start: 0.7350 (m) cc_final: 0.5923 (t) REVERT: A 509 GLN cc_start: 0.6070 (tp-100) cc_final: 0.5823 (tp-100) REVERT: A 627 ASP cc_start: 0.7495 (m-30) cc_final: 0.7152 (m-30) REVERT: C 15 MET cc_start: 0.7385 (tpp) cc_final: 0.7081 (tpp) REVERT: C 25 MET cc_start: 0.7020 (mmm) cc_final: 0.6422 (mmm) REVERT: C 53 ILE cc_start: 0.7270 (tp) cc_final: 0.6726 (pt) REVERT: C 70 LYS cc_start: 0.8322 (mttt) cc_final: 0.8033 (mttt) REVERT: C 132 LYS cc_start: 0.8418 (mttt) cc_final: 0.8213 (mttt) REVERT: C 161 MET cc_start: 0.6912 (mpp) cc_final: 0.6637 (mpp) REVERT: C 192 ARG cc_start: 0.8300 (mtm180) cc_final: 0.7997 (mtm-85) REVERT: C 221 GLU cc_start: 0.7919 (tp30) cc_final: 0.7703 (tp30) REVERT: C 254 GLU cc_start: 0.7425 (mp0) cc_final: 0.6873 (mp0) REVERT: C 469 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6835 (tp) REVERT: C 569 PHE cc_start: 0.7558 (t80) cc_final: 0.7328 (t80) REVERT: C 593 MET cc_start: 0.7960 (tpp) cc_final: 0.7519 (tpp) REVERT: C 679 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7991 (ttmt) REVERT: C 793 LYS cc_start: 0.8189 (mttp) cc_final: 0.7730 (mttm) REVERT: C 802 CYS cc_start: 0.7018 (m) cc_final: 0.6130 (t) REVERT: C 916 ILE cc_start: 0.8791 (pt) cc_final: 0.8290 (pt) REVERT: D 128 THR cc_start: 0.7388 (t) cc_final: 0.7180 (m) outliers start: 67 outliers final: 35 residues processed: 404 average time/residue: 0.2541 time to fit residues: 151.8002 Evaluate side-chains 389 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 353 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 650 GLU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 161 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 284 GLN A 343 HIS A 368 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN A 641 GLN A 700 HIS C 265 ASN C 299 ASN D 65 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131196 restraints weight = 30423.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135368 restraints weight = 17098.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.138185 restraints weight = 10885.062| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15236 Z= 0.147 Angle : 0.658 10.318 20639 Z= 0.327 Chirality : 0.041 0.179 2512 Planarity : 0.004 0.061 2611 Dihedral : 4.377 23.465 2057 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.55 % Allowed : 23.27 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1914 helix: 1.05 (0.16), residues: 1084 sheet: 1.11 (1.50), residues: 15 loop : -1.86 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 137 HIS 0.004 0.001 HIS A 343 PHE 0.026 0.001 PHE A 402 TYR 0.020 0.001 TYR A 260 ARG 0.008 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 729) hydrogen bonds : angle 4.56017 ( 2121) covalent geometry : bond 0.00330 (15236) covalent geometry : angle 0.65759 (20639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7106 (tp) cc_final: 0.6332 (tp) REVERT: A 117 LYS cc_start: 0.8676 (tttt) cc_final: 0.7939 (tptp) REVERT: A 235 GLN cc_start: 0.7212 (mp10) cc_final: 0.6657 (mp10) REVERT: A 239 ASP cc_start: 0.7258 (t0) cc_final: 0.6481 (t0) REVERT: A 242 ARG cc_start: 0.7667 (ptt90) cc_final: 0.7025 (ptt90) REVERT: A 271 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 281 GLU cc_start: 0.7315 (tp30) cc_final: 0.7037 (tp30) REVERT: A 290 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7980 (ptmm) REVERT: A 315 LYS cc_start: 0.7466 (mmtm) cc_final: 0.7070 (mmmm) REVERT: A 331 ASP cc_start: 0.7248 (t0) cc_final: 0.6871 (t0) REVERT: A 396 ASP cc_start: 0.7568 (m-30) cc_final: 0.7081 (m-30) REVERT: A 451 VAL cc_start: 0.8064 (t) cc_final: 0.7819 (t) REVERT: A 509 GLN cc_start: 0.6118 (tp-100) cc_final: 0.5880 (tp-100) REVERT: A 627 ASP cc_start: 0.7502 (m-30) cc_final: 0.7157 (m-30) REVERT: A 721 MET cc_start: 0.7681 (tpp) cc_final: 0.7446 (tpp) REVERT: C 29 ASP cc_start: 0.7767 (p0) cc_final: 0.7419 (m-30) REVERT: C 48 LYS cc_start: 0.8207 (mttp) cc_final: 0.7888 (mttp) REVERT: C 70 LYS cc_start: 0.8305 (mttt) cc_final: 0.8039 (mttt) REVERT: C 132 LYS cc_start: 0.8441 (mttt) cc_final: 0.8239 (mttt) REVERT: C 161 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6719 (mpp) REVERT: C 177 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7084 (tt) REVERT: C 192 ARG cc_start: 0.8387 (mtm180) cc_final: 0.8118 (mtm-85) REVERT: C 221 GLU cc_start: 0.7966 (tp30) cc_final: 0.7684 (tp30) REVERT: C 437 LYS cc_start: 0.7725 (ttpp) cc_final: 0.7464 (ptpp) REVERT: C 469 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6895 (tp) REVERT: C 494 LYS cc_start: 0.7782 (mtpt) cc_final: 0.7495 (mttp) REVERT: C 569 PHE cc_start: 0.7706 (t80) cc_final: 0.7418 (t80) REVERT: C 628 THR cc_start: 0.7994 (m) cc_final: 0.7730 (p) REVERT: C 679 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8140 (ttmt) REVERT: C 690 ILE cc_start: 0.7043 (mt) cc_final: 0.6647 (mm) REVERT: C 693 VAL cc_start: 0.8008 (t) cc_final: 0.7408 (p) REVERT: C 777 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8117 (mmp80) REVERT: C 793 LYS cc_start: 0.8275 (mttp) cc_final: 0.7871 (mttp) REVERT: C 802 CYS cc_start: 0.6994 (m) cc_final: 0.6194 (t) outliers start: 73 outliers final: 38 residues processed: 405 average time/residue: 0.2731 time to fit residues: 166.7456 Evaluate side-chains 391 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 350 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN A 700 HIS C 299 ASN D 49 ASN D 65 HIS E 236 ASN ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129866 restraints weight = 30337.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.134074 restraints weight = 17021.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.136918 restraints weight = 10847.973| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15236 Z= 0.148 Angle : 0.670 11.543 20639 Z= 0.329 Chirality : 0.040 0.169 2512 Planarity : 0.004 0.059 2611 Dihedral : 4.496 23.485 2057 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.18 % Allowed : 24.27 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1914 helix: 0.90 (0.16), residues: 1100 sheet: -0.84 (1.15), residues: 25 loop : -1.87 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.029 0.002 PHE A 498 TYR 0.015 0.001 TYR A 278 ARG 0.008 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 729) hydrogen bonds : angle 4.54255 ( 2121) covalent geometry : bond 0.00333 (15236) covalent geometry : angle 0.67016 (20639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 374 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8671 (tttt) cc_final: 0.7934 (tptp) REVERT: A 235 GLN cc_start: 0.7108 (mp10) cc_final: 0.6785 (mp10) REVERT: A 242 ARG cc_start: 0.7623 (ptt90) cc_final: 0.6978 (ptt90) REVERT: A 276 GLN cc_start: 0.7843 (pm20) cc_final: 0.7631 (pm20) REVERT: A 281 GLU cc_start: 0.7348 (tp30) cc_final: 0.7085 (tp30) REVERT: A 290 LYS cc_start: 0.8211 (ptmt) cc_final: 0.7849 (ptmm) REVERT: A 315 LYS cc_start: 0.7523 (mmtm) cc_final: 0.7129 (mmmm) REVERT: A 331 ASP cc_start: 0.7167 (t0) cc_final: 0.6861 (t0) REVERT: A 338 LYS cc_start: 0.8949 (tptp) cc_final: 0.8548 (tptp) REVERT: A 396 ASP cc_start: 0.7607 (m-30) cc_final: 0.7262 (m-30) REVERT: A 444 ASP cc_start: 0.6961 (t0) cc_final: 0.6736 (t70) REVERT: A 509 GLN cc_start: 0.6167 (tp-100) cc_final: 0.5950 (tp-100) REVERT: A 627 ASP cc_start: 0.7503 (m-30) cc_final: 0.7184 (m-30) REVERT: A 721 MET cc_start: 0.7672 (tpp) cc_final: 0.7448 (tpp) REVERT: C 29 ASP cc_start: 0.7729 (p0) cc_final: 0.7478 (m-30) REVERT: C 48 LYS cc_start: 0.8242 (mttp) cc_final: 0.7865 (mttp) REVERT: C 53 ILE cc_start: 0.7166 (tp) cc_final: 0.6571 (pt) REVERT: C 70 LYS cc_start: 0.8279 (mttt) cc_final: 0.7948 (mttt) REVERT: C 157 ILE cc_start: 0.8535 (tp) cc_final: 0.8160 (tp) REVERT: C 161 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6685 (mpp) REVERT: C 192 ARG cc_start: 0.8370 (mtm180) cc_final: 0.8121 (mtm-85) REVERT: C 265 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7392 (t0) REVERT: C 437 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7607 (ptpp) REVERT: C 469 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6947 (tp) REVERT: C 628 THR cc_start: 0.7941 (m) cc_final: 0.7653 (p) REVERT: C 634 LEU cc_start: 0.7691 (tt) cc_final: 0.7407 (tp) REVERT: C 679 LYS cc_start: 0.8283 (ttmt) cc_final: 0.8027 (ttmt) REVERT: C 690 ILE cc_start: 0.7194 (mt) cc_final: 0.6784 (mm) REVERT: C 693 VAL cc_start: 0.8009 (t) cc_final: 0.7404 (p) REVERT: C 777 ARG cc_start: 0.8321 (mmm160) cc_final: 0.7969 (mmp80) REVERT: C 793 LYS cc_start: 0.8381 (mttp) cc_final: 0.8033 (mttt) REVERT: C 802 CYS cc_start: 0.6804 (m) cc_final: 0.6119 (t) REVERT: C 915 GLU cc_start: 0.8585 (pp20) cc_final: 0.8015 (pp20) outliers start: 83 outliers final: 50 residues processed: 422 average time/residue: 0.2550 time to fit residues: 159.5084 Evaluate side-chains 418 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 365 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 150 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 184 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN D 65 HIS ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.151428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126963 restraints weight = 30424.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.131093 restraints weight = 17074.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.133898 restraints weight = 10890.758| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15236 Z= 0.159 Angle : 0.693 11.818 20639 Z= 0.338 Chirality : 0.041 0.169 2512 Planarity : 0.004 0.055 2611 Dihedral : 4.579 24.202 2057 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.18 % Allowed : 26.58 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1914 helix: 0.86 (0.16), residues: 1098 sheet: -0.95 (1.12), residues: 25 loop : -1.86 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 123 HIS 0.005 0.001 HIS D 64 PHE 0.028 0.002 PHE A 251 TYR 0.032 0.001 TYR A 260 ARG 0.008 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 729) hydrogen bonds : angle 4.61461 ( 2121) covalent geometry : bond 0.00354 (15236) covalent geometry : angle 0.69254 (20639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 376 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8637 (tttt) cc_final: 0.7894 (tptp) REVERT: A 235 GLN cc_start: 0.7056 (mp10) cc_final: 0.6690 (mp10) REVERT: A 237 LEU cc_start: 0.7778 (mt) cc_final: 0.7417 (mt) REVERT: A 242 ARG cc_start: 0.7709 (ptt90) cc_final: 0.7239 (ptt90) REVERT: A 263 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8494 (ttmm) REVERT: A 276 GLN cc_start: 0.7852 (pm20) cc_final: 0.7430 (pm20) REVERT: A 281 GLU cc_start: 0.7387 (tp30) cc_final: 0.7052 (tp30) REVERT: A 290 LYS cc_start: 0.8189 (ptmt) cc_final: 0.7844 (ptmt) REVERT: A 315 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7226 (mmmm) REVERT: A 324 ASN cc_start: 0.7984 (t0) cc_final: 0.7222 (p0) REVERT: A 331 ASP cc_start: 0.7225 (t0) cc_final: 0.6936 (t0) REVERT: A 338 LYS cc_start: 0.8925 (tptp) cc_final: 0.8690 (tptp) REVERT: A 627 ASP cc_start: 0.7526 (m-30) cc_final: 0.7200 (m-30) REVERT: A 705 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 29 ASP cc_start: 0.7654 (p0) cc_final: 0.7405 (m-30) REVERT: C 48 LYS cc_start: 0.8299 (mttp) cc_final: 0.7875 (mttp) REVERT: C 53 ILE cc_start: 0.7209 (tp) cc_final: 0.6598 (pt) REVERT: C 70 LYS cc_start: 0.8325 (mttt) cc_final: 0.7935 (mttt) REVERT: C 156 ASP cc_start: 0.8366 (m-30) cc_final: 0.8055 (m-30) REVERT: C 157 ILE cc_start: 0.8579 (tp) cc_final: 0.8227 (tp) REVERT: C 161 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6701 (mpp) REVERT: C 170 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.7094 (m) REVERT: C 192 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8156 (mtm-85) REVERT: C 437 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7604 (ptpp) REVERT: C 441 LYS cc_start: 0.8602 (mptt) cc_final: 0.8364 (mptt) REVERT: C 634 LEU cc_start: 0.7764 (tt) cc_final: 0.7494 (tp) REVERT: C 664 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6385 (tpp80) REVERT: C 679 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7949 (ttmt) REVERT: C 690 ILE cc_start: 0.7257 (mt) cc_final: 0.6854 (mm) REVERT: C 693 VAL cc_start: 0.7997 (t) cc_final: 0.7373 (p) REVERT: C 705 ASP cc_start: 0.7546 (t0) cc_final: 0.6419 (t0) REVERT: C 793 LYS cc_start: 0.8389 (mttp) cc_final: 0.7984 (mttp) REVERT: C 802 CYS cc_start: 0.6991 (m) cc_final: 0.6298 (t) REVERT: D 7 GLN cc_start: 0.7000 (mp10) cc_final: 0.6756 (mp10) REVERT: E 191 SER cc_start: 0.5147 (OUTLIER) cc_final: 0.3272 (p) outliers start: 83 outliers final: 52 residues processed: 425 average time/residue: 0.2651 time to fit residues: 165.1093 Evaluate side-chains 414 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 702 SER Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 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 386 ASN A 641 GLN A 700 HIS C 173 HIS C 265 ASN C 299 ASN D 65 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.151118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126834 restraints weight = 30409.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.130916 restraints weight = 17115.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.133651 restraints weight = 10941.179| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15236 Z= 0.156 Angle : 0.698 13.363 20639 Z= 0.340 Chirality : 0.041 0.146 2512 Planarity : 0.004 0.065 2611 Dihedral : 4.654 24.610 2057 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.86 % Allowed : 26.70 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1914 helix: 0.85 (0.16), residues: 1085 sheet: -1.10 (1.12), residues: 25 loop : -1.76 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 137 HIS 0.005 0.001 HIS D 64 PHE 0.023 0.002 PHE C 482 TYR 0.022 0.001 TYR A 260 ARG 0.011 0.001 ARG C 777 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 729) hydrogen bonds : angle 4.57306 ( 2121) covalent geometry : bond 0.00354 (15236) covalent geometry : angle 0.69756 (20639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 372 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.5767 (OUTLIER) cc_final: 0.5395 (m-70) REVERT: A 117 LYS cc_start: 0.8623 (tttt) cc_final: 0.7911 (tptp) REVERT: A 235 GLN cc_start: 0.7143 (mp10) cc_final: 0.6721 (mp10) REVERT: A 237 LEU cc_start: 0.7786 (mt) cc_final: 0.7406 (mt) REVERT: A 242 ARG cc_start: 0.7631 (ptt90) cc_final: 0.7144 (ptt90) REVERT: A 276 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 281 GLU cc_start: 0.7386 (tp30) cc_final: 0.7048 (tp30) REVERT: A 290 LYS cc_start: 0.8138 (ptmt) cc_final: 0.7829 (ptmt) REVERT: A 315 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7280 (mmtp) REVERT: A 324 ASN cc_start: 0.8013 (t0) cc_final: 0.7203 (p0) REVERT: A 331 ASP cc_start: 0.7244 (t0) cc_final: 0.6960 (t0) REVERT: A 338 LYS cc_start: 0.8894 (tptp) cc_final: 0.8671 (tptp) REVERT: A 451 VAL cc_start: 0.7927 (t) cc_final: 0.7700 (t) REVERT: A 627 ASP cc_start: 0.7524 (m-30) cc_final: 0.7193 (m-30) REVERT: A 705 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 29 ASP cc_start: 0.7655 (p0) cc_final: 0.7386 (m-30) REVERT: C 48 LYS cc_start: 0.8355 (mttp) cc_final: 0.8007 (mttp) REVERT: C 70 LYS cc_start: 0.8289 (mttt) cc_final: 0.7932 (mttt) REVERT: C 157 ILE cc_start: 0.8603 (tp) cc_final: 0.8264 (tp) REVERT: C 161 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6709 (mpp) REVERT: C 170 VAL cc_start: 0.7340 (OUTLIER) cc_final: 0.7109 (m) REVERT: C 192 ARG cc_start: 0.8427 (mtm180) cc_final: 0.8146 (mtm-85) REVERT: C 251 GLU cc_start: 0.7283 (pt0) cc_final: 0.6847 (pp20) REVERT: C 437 LYS cc_start: 0.7953 (ttpp) cc_final: 0.7667 (ptpp) REVERT: C 628 THR cc_start: 0.8133 (m) cc_final: 0.7805 (p) REVERT: C 634 LEU cc_start: 0.7743 (tt) cc_final: 0.7498 (tp) REVERT: C 664 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6302 (tpp80) REVERT: C 679 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7954 (ttmt) REVERT: C 690 ILE cc_start: 0.7270 (mt) cc_final: 0.6864 (mm) REVERT: C 693 VAL cc_start: 0.7992 (t) cc_final: 0.7371 (p) REVERT: C 705 ASP cc_start: 0.7555 (t0) cc_final: 0.6389 (t0) REVERT: C 793 LYS cc_start: 0.8335 (mttp) cc_final: 0.7922 (mttp) REVERT: C 802 CYS cc_start: 0.6987 (m) cc_final: 0.6271 (t) REVERT: E 191 SER cc_start: 0.5028 (OUTLIER) cc_final: 0.3046 (p) outliers start: 94 outliers final: 65 residues processed: 429 average time/residue: 0.2529 time to fit residues: 158.9844 Evaluate side-chains 434 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 363 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 757 ASP Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 84 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 476 HIS A 641 GLN A 700 HIS C 201 HIS C 299 ASN D 65 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.127511 restraints weight = 30244.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131710 restraints weight = 16834.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134479 restraints weight = 10687.433| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15236 Z= 0.147 Angle : 0.698 14.969 20639 Z= 0.338 Chirality : 0.040 0.178 2512 Planarity : 0.004 0.056 2611 Dihedral : 4.618 24.297 2057 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.24 % Allowed : 28.01 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1914 helix: 0.93 (0.16), residues: 1075 sheet: -1.11 (1.10), residues: 25 loop : -1.81 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.004 0.001 HIS A 727 PHE 0.016 0.001 PHE A 402 TYR 0.021 0.001 TYR A 260 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 729) hydrogen bonds : angle 4.53521 ( 2121) covalent geometry : bond 0.00335 (15236) covalent geometry : angle 0.69844 (20639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.5802 (OUTLIER) cc_final: 0.5416 (m-70) REVERT: A 117 LYS cc_start: 0.8602 (tttt) cc_final: 0.7815 (tptp) REVERT: A 235 GLN cc_start: 0.7163 (mp10) cc_final: 0.6735 (mp10) REVERT: A 237 LEU cc_start: 0.7755 (mt) cc_final: 0.7385 (mt) REVERT: A 242 ARG cc_start: 0.7598 (ptt90) cc_final: 0.7192 (ptt90) REVERT: A 263 LYS cc_start: 0.8706 (tttm) cc_final: 0.8496 (ttmm) REVERT: A 276 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: A 281 GLU cc_start: 0.7384 (tp30) cc_final: 0.7048 (tp30) REVERT: A 290 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7803 (ptmt) REVERT: A 315 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7267 (mmtp) REVERT: A 324 ASN cc_start: 0.8013 (t0) cc_final: 0.7180 (p0) REVERT: A 331 ASP cc_start: 0.7328 (t0) cc_final: 0.7037 (t0) REVERT: A 338 LYS cc_start: 0.8879 (tptp) cc_final: 0.8610 (tptp) REVERT: A 340 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8121 (tt) REVERT: A 444 ASP cc_start: 0.6945 (t0) cc_final: 0.6722 (t70) REVERT: A 451 VAL cc_start: 0.7951 (t) cc_final: 0.7733 (t) REVERT: A 509 GLN cc_start: 0.6252 (tp-100) cc_final: 0.6000 (tp-100) REVERT: A 627 ASP cc_start: 0.7528 (m-30) cc_final: 0.7195 (m-30) REVERT: A 705 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7093 (mm-30) REVERT: C 48 LYS cc_start: 0.8363 (mttp) cc_final: 0.7979 (mttp) REVERT: C 70 LYS cc_start: 0.8284 (mttt) cc_final: 0.7924 (mttt) REVERT: C 85 GLU cc_start: 0.8178 (mp0) cc_final: 0.7951 (mp0) REVERT: C 152 LEU cc_start: 0.8715 (mt) cc_final: 0.8453 (mt) REVERT: C 156 ASP cc_start: 0.8359 (m-30) cc_final: 0.8078 (m-30) REVERT: C 157 ILE cc_start: 0.8603 (tp) cc_final: 0.8269 (tp) REVERT: C 161 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6605 (mpp) REVERT: C 192 ARG cc_start: 0.8444 (mtm180) cc_final: 0.8157 (mtm-85) REVERT: C 251 GLU cc_start: 0.7341 (pt0) cc_final: 0.6845 (pp20) REVERT: C 437 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7617 (ptpp) REVERT: C 628 THR cc_start: 0.8097 (m) cc_final: 0.7839 (p) REVERT: C 634 LEU cc_start: 0.7751 (tt) cc_final: 0.7500 (tp) REVERT: C 690 ILE cc_start: 0.7306 (mt) cc_final: 0.6902 (mm) REVERT: C 693 VAL cc_start: 0.7998 (t) cc_final: 0.7371 (p) REVERT: C 705 ASP cc_start: 0.7540 (t0) cc_final: 0.6522 (t0) REVERT: C 793 LYS cc_start: 0.8349 (mttp) cc_final: 0.7932 (mttp) REVERT: C 802 CYS cc_start: 0.6941 (m) cc_final: 0.6223 (t) REVERT: E 138 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6919 (mm-40) REVERT: E 139 THR cc_start: 0.5237 (OUTLIER) cc_final: 0.4976 (p) REVERT: E 191 SER cc_start: 0.4999 (OUTLIER) cc_final: 0.2977 (p) outliers start: 84 outliers final: 60 residues processed: 415 average time/residue: 0.2642 time to fit residues: 161.2313 Evaluate side-chains 428 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 360 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 189 optimal weight: 0.0870 chunk 136 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN A 641 GLN A 700 HIS C 173 HIS C 299 ASN D 65 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.148084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.123950 restraints weight = 30391.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128008 restraints weight = 17135.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130720 restraints weight = 10996.296| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15236 Z= 0.211 Angle : 0.756 15.298 20639 Z= 0.376 Chirality : 0.043 0.187 2512 Planarity : 0.005 0.066 2611 Dihedral : 5.028 25.277 2057 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.74 % Allowed : 27.70 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1914 helix: 0.61 (0.16), residues: 1083 sheet: -1.34 (1.11), residues: 25 loop : -1.94 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 137 HIS 0.007 0.001 HIS C 508 PHE 0.024 0.002 PHE A 606 TYR 0.022 0.002 TYR A 260 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 729) hydrogen bonds : angle 4.84898 ( 2121) covalent geometry : bond 0.00468 (15236) covalent geometry : angle 0.75560 (20639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 377 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5617 (tmt170) REVERT: A 48 HIS cc_start: 0.6045 (OUTLIER) cc_final: 0.5652 (m-70) REVERT: A 117 LYS cc_start: 0.8657 (tttt) cc_final: 0.7935 (tptp) REVERT: A 139 TYR cc_start: 0.7802 (t80) cc_final: 0.7594 (t80) REVERT: A 229 LYS cc_start: 0.7124 (mtmm) cc_final: 0.6870 (mtmm) REVERT: A 235 GLN cc_start: 0.7075 (mp10) cc_final: 0.6654 (mp10) REVERT: A 237 LEU cc_start: 0.7954 (mt) cc_final: 0.7722 (mt) REVERT: A 274 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8390 (ttm110) REVERT: A 276 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: A 290 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7855 (ttpp) REVERT: A 315 LYS cc_start: 0.7628 (mmtm) cc_final: 0.7326 (mmtp) REVERT: A 324 ASN cc_start: 0.8066 (t0) cc_final: 0.7344 (p0) REVERT: A 331 ASP cc_start: 0.7427 (t0) cc_final: 0.7125 (t0) REVERT: A 338 LYS cc_start: 0.8916 (tptp) cc_final: 0.8561 (tptp) REVERT: A 340 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 444 ASP cc_start: 0.7022 (t0) cc_final: 0.6819 (t70) REVERT: A 627 ASP cc_start: 0.7532 (m-30) cc_final: 0.7215 (m-30) REVERT: A 725 LEU cc_start: 0.4931 (tp) cc_final: 0.4460 (tp) REVERT: C 48 LYS cc_start: 0.8416 (mttp) cc_final: 0.8039 (mttp) REVERT: C 70 LYS cc_start: 0.8305 (mttt) cc_final: 0.7930 (mttt) REVERT: C 85 GLU cc_start: 0.8150 (mp0) cc_final: 0.7873 (mp0) REVERT: C 157 ILE cc_start: 0.8613 (tp) cc_final: 0.8272 (tp) REVERT: C 161 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6577 (mpp) REVERT: C 192 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8173 (mtm-85) REVERT: C 251 GLU cc_start: 0.7509 (pt0) cc_final: 0.6937 (pp20) REVERT: C 265 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7512 (t0) REVERT: C 437 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7682 (ptpp) REVERT: C 664 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6181 (tpp80) REVERT: C 679 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7971 (ttmt) REVERT: C 690 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6970 (mm) REVERT: C 693 VAL cc_start: 0.8126 (t) cc_final: 0.7490 (p) REVERT: C 705 ASP cc_start: 0.7541 (t0) cc_final: 0.6298 (t0) REVERT: C 793 LYS cc_start: 0.8310 (mttp) cc_final: 0.7933 (mttp) REVERT: C 802 CYS cc_start: 0.6976 (m) cc_final: 0.6180 (t) REVERT: E 138 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.6950 (mt0) REVERT: E 139 THR cc_start: 0.5303 (OUTLIER) cc_final: 0.5076 (p) outliers start: 92 outliers final: 63 residues processed: 429 average time/residue: 0.2696 time to fit residues: 168.8947 Evaluate side-chains 445 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 371 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 753 SER Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 412 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.0040 chunk 188 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 chunk 107 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN A 700 HIS C 173 HIS C 514 HIS C 931 ASN D 64 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.151593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127579 restraints weight = 30083.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131817 restraints weight = 16705.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.134609 restraints weight = 10558.564| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15236 Z= 0.141 Angle : 0.737 17.072 20639 Z= 0.357 Chirality : 0.041 0.190 2512 Planarity : 0.004 0.069 2611 Dihedral : 4.757 24.491 2057 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.55 % Allowed : 29.94 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1914 helix: 0.84 (0.16), residues: 1075 sheet: -0.62 (1.30), residues: 20 loop : -1.77 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 123 HIS 0.004 0.001 HIS D 65 PHE 0.015 0.001 PHE A 402 TYR 0.032 0.001 TYR A 260 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 729) hydrogen bonds : angle 4.65534 ( 2121) covalent geometry : bond 0.00323 (15236) covalent geometry : angle 0.73714 (20639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.5997 (OUTLIER) cc_final: 0.5561 (m-70) REVERT: A 117 LYS cc_start: 0.8611 (tttt) cc_final: 0.7816 (tptp) REVERT: A 235 GLN cc_start: 0.7154 (mp10) cc_final: 0.6700 (mp10) REVERT: A 242 ARG cc_start: 0.7640 (ptt90) cc_final: 0.7350 (ptt90) REVERT: A 253 GLN cc_start: 0.7745 (mt0) cc_final: 0.7452 (mt0) REVERT: A 276 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: A 315 LYS cc_start: 0.7534 (mmtm) cc_final: 0.7303 (mmtp) REVERT: A 324 ASN cc_start: 0.8004 (t0) cc_final: 0.7192 (p0) REVERT: A 331 ASP cc_start: 0.7414 (t0) cc_final: 0.7072 (t0) REVERT: A 338 LYS cc_start: 0.8855 (tptp) cc_final: 0.8516 (tptp) REVERT: A 340 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8228 (tt) REVERT: A 606 PHE cc_start: 0.4801 (m-10) cc_final: 0.4444 (m-10) REVERT: A 705 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 719 MET cc_start: 0.5550 (mtt) cc_final: 0.5334 (mtp) REVERT: A 725 LEU cc_start: 0.4958 (tp) cc_final: 0.4518 (tp) REVERT: C 48 LYS cc_start: 0.8397 (mttp) cc_final: 0.7962 (mttp) REVERT: C 70 LYS cc_start: 0.8279 (mttt) cc_final: 0.7890 (mttt) REVERT: C 85 GLU cc_start: 0.8172 (mp0) cc_final: 0.7553 (mp0) REVERT: C 89 ASP cc_start: 0.7173 (m-30) cc_final: 0.6963 (m-30) REVERT: C 157 ILE cc_start: 0.8604 (tp) cc_final: 0.8258 (tp) REVERT: C 161 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6591 (mpp) REVERT: C 192 ARG cc_start: 0.8437 (mtm180) cc_final: 0.8165 (mtm-85) REVERT: C 251 GLU cc_start: 0.7493 (pt0) cc_final: 0.6900 (pp20) REVERT: C 437 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7557 (ptpp) REVERT: C 569 PHE cc_start: 0.7786 (t80) cc_final: 0.7365 (t80) REVERT: C 634 LEU cc_start: 0.7756 (tt) cc_final: 0.7523 (tp) REVERT: C 664 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.5862 (tpp80) REVERT: C 679 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7969 (ttmt) REVERT: C 690 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6965 (mm) REVERT: C 693 VAL cc_start: 0.8044 (t) cc_final: 0.7403 (p) REVERT: C 705 ASP cc_start: 0.7512 (t0) cc_final: 0.6212 (t0) REVERT: C 793 LYS cc_start: 0.8277 (mttp) cc_final: 0.7870 (mttp) REVERT: C 802 CYS cc_start: 0.6920 (m) cc_final: 0.6153 (t) REVERT: E 138 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6927 (mm-40) REVERT: E 139 THR cc_start: 0.5198 (OUTLIER) cc_final: 0.4925 (p) REVERT: E 219 SER cc_start: 0.7905 (p) cc_final: 0.7415 (m) outliers start: 73 outliers final: 57 residues processed: 419 average time/residue: 0.2596 time to fit residues: 158.6697 Evaluate side-chains 431 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 366 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 664 ARG Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 126 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 ASN A 700 HIS C 173 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.149214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125133 restraints weight = 30147.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129325 restraints weight = 16794.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.132103 restraints weight = 10661.868| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15236 Z= 0.199 Angle : 0.776 17.116 20639 Z= 0.379 Chirality : 0.043 0.238 2512 Planarity : 0.005 0.072 2611 Dihedral : 4.981 25.571 2057 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.55 % Allowed : 29.51 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1914 helix: 0.64 (0.16), residues: 1081 sheet: -1.17 (1.13), residues: 25 loop : -1.89 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 61 HIS 0.006 0.001 HIS A 727 PHE 0.024 0.002 PHE A 606 TYR 0.037 0.002 TYR A 260 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 729) hydrogen bonds : angle 4.86028 ( 2121) covalent geometry : bond 0.00448 (15236) covalent geometry : angle 0.77630 (20639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 384 time to evaluate : 1.645 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 41 ARG cc_start: 0.5990 (OUTLIER) cc_final: 0.5691 (tmt170) REVERT: A 117 LYS cc_start: 0.8613 (tttt) cc_final: 0.7831 (tptp) REVERT: A 235 GLN cc_start: 0.7025 (mp10) cc_final: 0.6538 (mp10) REVERT: A 242 ARG cc_start: 0.7671 (ptt90) cc_final: 0.7397 (ptt90) REVERT: A 253 GLN cc_start: 0.7741 (mt0) cc_final: 0.7527 (mt0) REVERT: A 315 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7381 (mmtp) REVERT: A 324 ASN cc_start: 0.8065 (t0) cc_final: 0.7318 (p0) REVERT: A 331 ASP cc_start: 0.7444 (t0) cc_final: 0.7075 (t0) REVERT: A 338 LYS cc_start: 0.8876 (tptp) cc_final: 0.8544 (tptp) REVERT: A 340 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8255 (tt) REVERT: A 451 VAL cc_start: 0.8071 (t) cc_final: 0.7864 (t) REVERT: A 498 PHE cc_start: 0.7285 (t80) cc_final: 0.6952 (t80) REVERT: A 627 ASP cc_start: 0.7551 (m-30) cc_final: 0.7207 (m-30) REVERT: A 705 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 725 LEU cc_start: 0.5025 (tp) cc_final: 0.4557 (tp) REVERT: C 48 LYS cc_start: 0.8420 (mttp) cc_final: 0.8016 (mttp) REVERT: C 70 LYS cc_start: 0.8260 (mttt) cc_final: 0.7868 (mttt) REVERT: C 85 GLU cc_start: 0.8159 (mp0) cc_final: 0.7880 (mp0) REVERT: C 157 ILE cc_start: 0.8608 (tp) cc_final: 0.8266 (tp) REVERT: C 161 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6593 (mpp) REVERT: C 192 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8116 (mtm-85) REVERT: C 221 GLU cc_start: 0.7967 (tp30) cc_final: 0.7648 (tp30) REVERT: C 251 GLU cc_start: 0.7499 (pt0) cc_final: 0.6903 (pp20) REVERT: C 437 LYS cc_start: 0.7926 (ttpp) cc_final: 0.7598 (ptpp) REVERT: C 634 LEU cc_start: 0.7825 (tt) cc_final: 0.7588 (tp) REVERT: C 679 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7963 (ttmt) REVERT: C 690 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7062 (mm) REVERT: C 693 VAL cc_start: 0.8108 (t) cc_final: 0.7458 (p) REVERT: C 705 ASP cc_start: 0.7483 (t0) cc_final: 0.6324 (t0) REVERT: C 793 LYS cc_start: 0.8284 (mttp) cc_final: 0.7903 (mttp) REVERT: E 138 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: E 139 THR cc_start: 0.5321 (OUTLIER) cc_final: 0.5081 (p) outliers start: 73 outliers final: 59 residues processed: 426 average time/residue: 0.2791 time to fit residues: 174.4448 Evaluate side-chains 441 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 376 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 689 LYS Chi-restraints excluded: chain A residue 694 GLN Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 792 HIS Chi-restraints excluded: chain C residue 872 VAL Chi-restraints excluded: chain C residue 933 TRP Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 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 368 GLN A 641 GLN A 700 HIS C 173 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.150155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126224 restraints weight = 30007.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.130415 restraints weight = 16683.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.133299 restraints weight = 10575.051| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15236 Z= 0.167 Angle : 0.783 17.658 20639 Z= 0.378 Chirality : 0.043 0.248 2512 Planarity : 0.005 0.071 2611 Dihedral : 4.915 25.169 2057 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 4.18 % Allowed : 30.19 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1914 helix: 0.69 (0.16), residues: 1081 sheet: -0.41 (1.36), residues: 20 loop : -1.89 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 123 HIS 0.005 0.001 HIS A 727 PHE 0.020 0.002 PHE A 547 TYR 0.030 0.002 TYR A 260 ARG 0.009 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 729) hydrogen bonds : angle 4.79050 ( 2121) covalent geometry : bond 0.00389 (15236) covalent geometry : angle 0.78251 (20639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6699.62 seconds wall clock time: 115 minutes 54.74 seconds (6954.74 seconds total)