Starting phenix.real_space_refine on Sat May 17 01:04:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or4_17117/05_2025/8or4_17117.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or4_17117/05_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_17117/05_2025/8or4_17117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or4_17117/05_2025/8or4_17117.map" model { file = "/net/cci-nas-00/data/ceres_data/8or4_17117/05_2025/8or4_17117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or4_17117/05_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-5687/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: 8.30, per 1000 atoms: 0.55 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: 3.67 Conformation dependent library (CDL) restraints added in 1.8 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: 1.39 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: 3.94 Time building geometry restraints manager: 4.28 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 32.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- 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 : 1.604 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: 0.2582 time to fit residues: 136.5322 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 : 1.601 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135249 restraints weight = 30860.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.139420 restraints weight = 17153.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.142224 restraints weight = 10831.627| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 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 : 1.620 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: 0.6442 (tp) REVERT: A 117 LYS cc_start: 0.8608 (tttt) cc_final: 0.7981 (tptp) REVERT: A 123 TRP cc_start: 0.7165 (t60) cc_final: 0.6793 (t60) REVERT: A 271 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 315 LYS cc_start: 0.7292 (mmtm) cc_final: 0.7002 (mmtp) REVERT: A 331 ASP cc_start: 0.7190 (t0) cc_final: 0.6880 (t0) REVERT: A 451 VAL cc_start: 0.8132 (t) cc_final: 0.7917 (t) REVERT: A 469 MET cc_start: 0.6755 (tpp) cc_final: 0.6478 (tpp) REVERT: A 501 THR cc_start: 0.7350 (m) cc_final: 0.5924 (t) REVERT: A 509 GLN cc_start: 0.6072 (tp-100) cc_final: 0.5824 (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: 0.6421 (mmm) REVERT: C 53 ILE cc_start: 0.7271 (tp) cc_final: 0.6727 (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: 0.6916 (mpp) cc_final: 0.6639 (mpp) REVERT: C 192 ARG cc_start: 0.8302 (mtm180) cc_final: 0.7998 (mtm-85) REVERT: C 221 GLU cc_start: 0.7920 (tp30) cc_final: 0.7703 (tp30) REVERT: C 254 GLU cc_start: 0.7425 (mp0) cc_final: 0.6872 (mp0) REVERT: C 469 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6834 (tp) REVERT: C 569 PHE cc_start: 0.7557 (t80) cc_final: 0.7327 (t80) REVERT: C 593 MET cc_start: 0.7962 (tpp) cc_final: 0.7520 (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: 0.7020 (m) cc_final: 0.6132 (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: 0.7179 (m) outliers start: 67 outliers final: 35 residues processed: 404 average time/residue: 0.2572 time to fit residues: 153.6784 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 : 1.546 ------------------------------------------------------------------------------- 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: 0.2980 chunk 20 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 0.0030 chunk 71 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 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 = 0.4195 r_free = 0.4195 target = 0.156016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.131859 restraints weight = 30567.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.136020 restraints weight = 17204.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.138791 restraints weight = 10968.601| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15236 Z= 0.134 Angle : 0.647 10.288 20639 Z= 0.320 Chirality : 0.040 0.157 2512 Planarity : 0.004 0.060 2611 Dihedral : 4.316 23.006 2057 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.43 % Allowed : 23.14 % Favored : 72.43 % 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: -0.14 (0.20), residues: 1914 helix: 1.09 (0.16), residues: 1080 sheet: 1.10 (1.51), residues: 15 loop : -1.79 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 137 HIS 0.004 0.001 HIS C 173 PHE 0.026 0.001 PHE A 402 TYR 0.019 0.001 TYR A 260 ARG 0.007 0.001 ARG E 234 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 729) hydrogen bonds : angle 4.50705 ( 2121) covalent geometry : bond 0.00302 (15236) covalent geometry : angle 0.64737 (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 439 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 368 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7091 (tp) cc_final: 0.6279 (tp) REVERT: A 117 LYS cc_start: 0.8665 (tttt) cc_final: 0.7932 (tptp) REVERT: A 235 GLN cc_start: 0.7189 (mp10) cc_final: 0.6605 (mp10) REVERT: A 239 ASP cc_start: 0.7213 (t0) cc_final: 0.6557 (t0) REVERT: A 242 ARG cc_start: 0.7652 (ptt90) cc_final: 0.7007 (ptt90) REVERT: A 271 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 281 GLU cc_start: 0.7288 (tp30) cc_final: 0.7009 (tp30) REVERT: A 290 LYS cc_start: 0.8195 (ptmt) cc_final: 0.7932 (ptmm) REVERT: A 315 LYS cc_start: 0.7370 (mmtm) cc_final: 0.6973 (mmmm) REVERT: A 331 ASP cc_start: 0.7215 (t0) cc_final: 0.6833 (t0) REVERT: A 377 TYR cc_start: 0.8402 (m-80) cc_final: 0.7954 (m-80) REVERT: A 396 ASP cc_start: 0.7579 (m-30) cc_final: 0.7053 (m-30) REVERT: A 451 VAL cc_start: 0.8070 (t) cc_final: 0.7823 (t) REVERT: A 482 ASP cc_start: 0.6379 (m-30) cc_final: 0.6136 (m-30) REVERT: A 509 GLN cc_start: 0.6093 (tp-100) cc_final: 0.5851 (tp-100) REVERT: A 627 ASP cc_start: 0.7505 (m-30) cc_final: 0.7158 (m-30) REVERT: A 721 MET cc_start: 0.7664 (tpp) cc_final: 0.7419 (tpp) REVERT: C 15 MET cc_start: 0.7461 (tpp) cc_final: 0.7257 (tpp) REVERT: C 29 ASP cc_start: 0.7756 (p0) cc_final: 0.7405 (m-30) REVERT: C 48 LYS cc_start: 0.8197 (mttp) cc_final: 0.7964 (mttp) REVERT: C 70 LYS cc_start: 0.8262 (mttt) cc_final: 0.7930 (mttt) REVERT: C 157 ILE cc_start: 0.8426 (tp) cc_final: 0.8029 (tp) REVERT: C 161 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6714 (mpp) REVERT: C 192 ARG cc_start: 0.8343 (mtm180) cc_final: 0.8074 (mtm-85) REVERT: C 221 GLU cc_start: 0.7933 (tp30) cc_final: 0.7636 (tp30) REVERT: C 253 LEU cc_start: 0.8624 (pp) cc_final: 0.8165 (pp) REVERT: C 254 GLU cc_start: 0.7180 (mp0) cc_final: 0.6899 (mp0) REVERT: C 437 LYS cc_start: 0.7728 (ttpp) cc_final: 0.7489 (ptpp) REVERT: C 469 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6877 (tp) REVERT: C 569 PHE cc_start: 0.7697 (t80) cc_final: 0.7414 (t80) REVERT: C 628 THR cc_start: 0.7958 (m) cc_final: 0.7689 (p) REVERT: C 679 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8140 (ttmt) REVERT: C 690 ILE cc_start: 0.7052 (mt) cc_final: 0.6658 (mm) REVERT: C 693 VAL cc_start: 0.7974 (t) cc_final: 0.7372 (p) REVERT: C 777 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8106 (mmp80) REVERT: C 793 LYS cc_start: 0.8272 (mttp) cc_final: 0.7855 (mttm) REVERT: C 802 CYS cc_start: 0.6968 (m) cc_final: 0.6194 (t) outliers start: 71 outliers final: 38 residues processed: 407 average time/residue: 0.2766 time to fit residues: 169.1792 Evaluate side-chains 388 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 348 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 326 VAL 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 C residue 41 LEU Chi-restraints excluded: chain C residue 63 GLU 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 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 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 780 THR 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 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: 3.9990 chunk 47 optimal weight: 0.0770 chunk 143 optimal weight: 0.0030 chunk 87 optimal weight: 0.7980 chunk 164 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.4748 ------------------------------------------------------------------------------- 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 A 505 GLN A 641 GLN A 700 HIS C 299 ASN D 49 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 = 0.4190 r_free = 0.4190 target = 0.155578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131439 restraints weight = 30668.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.135598 restraints weight = 17278.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.138348 restraints weight = 11014.141| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2336 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= 0.130 Angle : 0.655 11.025 20639 Z= 0.320 Chirality : 0.039 0.142 2512 Planarity : 0.004 0.059 2611 Dihedral : 4.342 22.653 2057 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.80 % Allowed : 24.95 % Favored : 70.24 % 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: -0.25 (0.20), residues: 1914 helix: 1.01 (0.16), residues: 1089 sheet: -0.81 (1.11), residues: 25 loop : -1.87 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.030 0.001 PHE A 498 TYR 0.016 0.001 TYR A 99 ARG 0.007 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 729) hydrogen bonds : angle 4.47147 ( 2121) covalent geometry : bond 0.00294 (15236) covalent geometry : angle 0.65511 (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 448 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 371 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8647 (tttt) cc_final: 0.7934 (tptp) REVERT: A 235 GLN cc_start: 0.7076 (mp10) cc_final: 0.6754 (mp10) REVERT: A 242 ARG cc_start: 0.7609 (ptt90) cc_final: 0.6945 (ptt90) REVERT: A 271 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7282 (mt-10) REVERT: A 276 GLN cc_start: 0.7823 (pm20) cc_final: 0.7604 (pm20) REVERT: A 281 GLU cc_start: 0.7311 (tp30) cc_final: 0.7044 (tp30) REVERT: A 290 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7934 (ttpp) REVERT: A 315 LYS cc_start: 0.7376 (mmtm) cc_final: 0.6999 (mmmm) REVERT: A 331 ASP cc_start: 0.7161 (t0) cc_final: 0.6831 (t0) REVERT: A 396 ASP cc_start: 0.7551 (m-30) cc_final: 0.7006 (m-30) REVERT: A 444 ASP cc_start: 0.6881 (t0) cc_final: 0.6674 (t70) REVERT: A 451 VAL cc_start: 0.8049 (t) cc_final: 0.7841 (t) REVERT: A 509 GLN cc_start: 0.6112 (tp-100) cc_final: 0.5900 (tp-100) REVERT: A 627 ASP cc_start: 0.7495 (m-30) cc_final: 0.7168 (m-30) REVERT: A 705 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 29 ASP cc_start: 0.7717 (p0) cc_final: 0.7384 (m-30) REVERT: C 48 LYS cc_start: 0.8235 (mttp) cc_final: 0.7883 (mttp) REVERT: C 53 ILE cc_start: 0.7141 (tp) cc_final: 0.6551 (pt) REVERT: C 70 LYS cc_start: 0.8290 (mttt) cc_final: 0.7998 (mttt) REVERT: C 157 ILE cc_start: 0.8460 (tp) cc_final: 0.8139 (tp) REVERT: C 161 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6541 (mpp) REVERT: C 192 ARG cc_start: 0.8341 (mtm180) cc_final: 0.8088 (mtm-85) REVERT: C 221 GLU cc_start: 0.7919 (tp30) cc_final: 0.7600 (tp30) REVERT: C 441 LYS cc_start: 0.8593 (mptt) cc_final: 0.8377 (mptt) REVERT: C 469 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6895 (tp) REVERT: C 494 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7505 (mttp) REVERT: C 569 PHE cc_start: 0.7773 (t80) cc_final: 0.7443 (t80) REVERT: C 593 MET cc_start: 0.8013 (tpp) cc_final: 0.7474 (tpp) REVERT: C 628 THR cc_start: 0.7953 (m) cc_final: 0.7665 (p) REVERT: C 634 LEU cc_start: 0.7660 (tt) cc_final: 0.7340 (tp) REVERT: C 679 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8024 (ttmt) REVERT: C 690 ILE cc_start: 0.7123 (mt) cc_final: 0.6659 (mm) REVERT: C 693 VAL cc_start: 0.7976 (t) cc_final: 0.7412 (p) REVERT: C 777 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7987 (mmp80) REVERT: C 793 LYS cc_start: 0.8368 (mttp) cc_final: 0.8028 (mttt) REVERT: C 802 CYS cc_start: 0.6841 (m) cc_final: 0.6115 (t) REVERT: E 222 ILE cc_start: 0.8315 (tp) cc_final: 0.8052 (tp) outliers start: 77 outliers final: 48 residues processed: 420 average time/residue: 0.2587 time to fit residues: 160.7664 Evaluate side-chains 410 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 268 LEU 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 475 VAL 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 738 LEU 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 37 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU 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 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 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 137 THR Chi-restraints excluded: chain E residue 137 TRP Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 188 LEU 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: 0.0270 chunk 75 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN D 65 HIS E 236 ASN ** 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 = 0.4173 r_free = 0.4173 target = 0.154113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.129582 restraints weight = 30352.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.133786 restraints weight = 16994.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.136607 restraints weight = 10801.325| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15236 Z= 0.135 Angle : 0.664 11.663 20639 Z= 0.322 Chirality : 0.040 0.168 2512 Planarity : 0.004 0.057 2611 Dihedral : 4.346 22.877 2057 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.87 % Allowed : 25.76 % Favored : 69.37 % 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: -0.23 (0.20), residues: 1914 helix: 1.01 (0.16), residues: 1100 sheet: -0.88 (1.12), residues: 25 loop : -1.86 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 123 HIS 0.004 0.001 HIS A 343 PHE 0.021 0.001 PHE A 498 TYR 0.029 0.001 TYR A 260 ARG 0.007 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 729) hydrogen bonds : angle 4.44132 ( 2121) covalent geometry : bond 0.00301 (15236) covalent geometry : angle 0.66446 (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 451 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 373 time to evaluate : 1.595 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: 0.8641 (tttt) cc_final: 0.7903 (tptp) REVERT: A 235 GLN cc_start: 0.7048 (mp10) cc_final: 0.6648 (mp10) REVERT: A 242 ARG cc_start: 0.7736 (ptt90) cc_final: 0.7260 (ptt90) REVERT: A 276 GLN cc_start: 0.7828 (pm20) cc_final: 0.7418 (pm20) REVERT: A 290 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7933 (ttpp) REVERT: A 315 LYS cc_start: 0.7488 (mmtm) cc_final: 0.7097 (mmmm) REVERT: A 331 ASP cc_start: 0.7180 (t0) cc_final: 0.6873 (t0) REVERT: A 338 LYS cc_start: 0.8896 (tptp) cc_final: 0.8432 (tptp) REVERT: A 340 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 444 ASP cc_start: 0.6911 (t70) cc_final: 0.6696 (t70) REVERT: A 451 VAL cc_start: 0.7997 (t) cc_final: 0.7780 (t) REVERT: A 475 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7709 (t) REVERT: A 509 GLN cc_start: 0.6223 (tp-100) cc_final: 0.5966 (tp-100) REVERT: A 627 ASP cc_start: 0.7509 (m-30) cc_final: 0.7187 (m-30) REVERT: A 705 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 29 ASP cc_start: 0.7689 (p0) cc_final: 0.7437 (m-30) REVERT: C 48 LYS cc_start: 0.8263 (mttp) cc_final: 0.7847 (mttp) REVERT: C 70 LYS cc_start: 0.8295 (mttt) cc_final: 0.7942 (mttt) REVERT: C 157 ILE cc_start: 0.8524 (tp) cc_final: 0.8234 (tp) REVERT: C 161 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6676 (mpp) REVERT: C 192 ARG cc_start: 0.8438 (mtm180) cc_final: 0.8133 (mtm-85) REVERT: C 221 GLU cc_start: 0.7949 (tp30) cc_final: 0.7614 (tp30) REVERT: C 469 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6894 (tp) REVERT: C 593 MET cc_start: 0.8034 (tpp) cc_final: 0.7478 (tpp) REVERT: C 628 THR cc_start: 0.7975 (m) cc_final: 0.7653 (p) REVERT: C 634 LEU cc_start: 0.7688 (tt) cc_final: 0.7382 (tp) REVERT: C 679 LYS cc_start: 0.8300 (ttmt) cc_final: 0.8056 (ttmt) REVERT: C 690 ILE cc_start: 0.7215 (mt) cc_final: 0.6765 (mm) REVERT: C 693 VAL cc_start: 0.7998 (t) cc_final: 0.7476 (p) REVERT: C 793 LYS cc_start: 0.8357 (mttp) cc_final: 0.8147 (mttm) REVERT: C 802 CYS cc_start: 0.7014 (m) cc_final: 0.6329 (t) REVERT: E 191 SER cc_start: 0.4955 (OUTLIER) cc_final: 0.2948 (p) REVERT: E 222 ILE cc_start: 0.8300 (tp) cc_final: 0.8052 (tp) outliers start: 78 outliers final: 52 residues processed: 417 average time/residue: 0.2581 time to fit residues: 158.1453 Evaluate side-chains 420 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 363 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 THR Chi-restraints excluded: chain A residue 268 LEU 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 340 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 475 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 604 SER 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 A residue 721 MET Chi-restraints excluded: chain A residue 738 LEU 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 96 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 180 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 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 702 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 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 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: 1.9990 chunk 31 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 641 GLN A 700 HIS 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 = 0.4162 r_free = 0.4162 target = 0.153396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129146 restraints weight = 30421.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133229 restraints weight = 17143.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.135925 restraints weight = 10944.991| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.138 Angle : 0.671 12.524 20639 Z= 0.325 Chirality : 0.040 0.148 2512 Planarity : 0.004 0.067 2611 Dihedral : 4.393 23.227 2057 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.43 % Allowed : 26.82 % Favored : 67.75 % 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: -0.22 (0.20), residues: 1914 helix: 1.01 (0.16), residues: 1086 sheet: -0.86 (1.11), residues: 25 loop : -1.78 (0.23), residues: 803 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 0.023 0.001 PHE C 482 TYR 0.022 0.001 TYR A 260 ARG 0.010 0.001 ARG C 777 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 729) hydrogen bonds : angle 4.47511 ( 2121) covalent geometry : bond 0.00314 (15236) covalent geometry : angle 0.67067 (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 457 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 370 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8620 (tttt) cc_final: 0.7910 (tptp) REVERT: A 235 GLN cc_start: 0.7060 (mp10) cc_final: 0.6632 (mp10) REVERT: A 237 LEU cc_start: 0.7805 (mt) cc_final: 0.7599 (mt) REVERT: A 242 ARG cc_start: 0.7677 (ptt90) cc_final: 0.7164 (ptt90) REVERT: A 276 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: A 290 LYS cc_start: 0.8104 (ptmt) cc_final: 0.7893 (ttpp) REVERT: A 315 LYS cc_start: 0.7506 (mmtm) cc_final: 0.7146 (mmmm) REVERT: A 331 ASP cc_start: 0.7220 (t0) cc_final: 0.6933 (t0) REVERT: A 340 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8205 (tt) REVERT: A 450 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7147 (mmm) REVERT: A 451 VAL cc_start: 0.7992 (t) cc_final: 0.7790 (t) REVERT: A 509 GLN cc_start: 0.6187 (tp-100) cc_final: 0.5934 (tp-100) REVERT: A 705 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 721 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7450 (tpp) REVERT: C 48 LYS cc_start: 0.8319 (mttp) cc_final: 0.7968 (mttp) REVERT: C 70 LYS cc_start: 0.8339 (mttt) cc_final: 0.7986 (mttt) REVERT: C 156 ASP cc_start: 0.8310 (m-30) cc_final: 0.7965 (m-30) REVERT: C 157 ILE cc_start: 0.8528 (tp) cc_final: 0.8225 (tp) REVERT: C 161 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6625 (mpp) REVERT: C 192 ARG cc_start: 0.8423 (mtm180) cc_final: 0.8127 (mtm-85) REVERT: C 221 GLU cc_start: 0.7963 (tp30) cc_final: 0.7620 (tp30) REVERT: C 469 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6956 (tp) REVERT: C 569 PHE cc_start: 0.7799 (t80) cc_final: 0.7357 (t80) REVERT: C 634 LEU cc_start: 0.7712 (tt) cc_final: 0.7435 (tp) REVERT: C 679 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7979 (ttmt) REVERT: C 690 ILE cc_start: 0.7289 (mt) cc_final: 0.6841 (mm) REVERT: C 693 VAL cc_start: 0.7975 (t) cc_final: 0.7347 (p) REVERT: C 705 ASP cc_start: 0.7553 (t0) cc_final: 0.6520 (t0) REVERT: C 793 LYS cc_start: 0.8363 (mttp) cc_final: 0.8137 (mttm) REVERT: C 802 CYS cc_start: 0.6983 (m) cc_final: 0.6305 (t) REVERT: E 222 ILE cc_start: 0.8268 (tp) cc_final: 0.8015 (tp) outliers start: 87 outliers final: 60 residues processed: 418 average time/residue: 0.2519 time to fit residues: 154.1461 Evaluate side-chains 427 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 361 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 THR Chi-restraints excluded: chain A residue 268 LEU 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 340 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET 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 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 721 MET 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 63 GLU 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 172 PHE 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 306 THR 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 571 CYS 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 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 132 SER 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: 0.7980 chunk 18 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 183 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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** ** 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 = 0.4156 r_free = 0.4156 target = 0.152789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.128505 restraints weight = 30654.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.132628 restraints weight = 17288.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.135415 restraints weight = 11069.130| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15236 Z= 0.135 Angle : 0.681 14.274 20639 Z= 0.330 Chirality : 0.040 0.190 2512 Planarity : 0.004 0.057 2611 Dihedral : 4.410 23.238 2057 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.18 % Allowed : 27.45 % Favored : 67.37 % 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: -0.18 (0.20), residues: 1914 helix: 1.04 (0.16), residues: 1084 sheet: -0.91 (1.11), residues: 25 loop : -1.76 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 123 HIS 0.005 0.001 HIS C 173 PHE 0.017 0.001 PHE A 402 TYR 0.019 0.001 TYR A 260 ARG 0.007 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 729) hydrogen bonds : angle 4.45968 ( 2121) covalent geometry : bond 0.00309 (15236) covalent geometry : angle 0.68110 (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: 83 poor density : 370 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8564 (tttt) cc_final: 0.7805 (tptp) REVERT: A 235 GLN cc_start: 0.7042 (mp10) cc_final: 0.6627 (mp10) REVERT: A 242 ARG cc_start: 0.7598 (ptt90) cc_final: 0.7142 (ptt90) REVERT: A 250 GLU cc_start: 0.7526 (pm20) cc_final: 0.6760 (pm20) REVERT: A 276 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: A 290 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7912 (ttpp) REVERT: A 315 LYS cc_start: 0.7499 (mmtm) cc_final: 0.7141 (mmmm) REVERT: A 324 ASN cc_start: 0.7966 (t0) cc_final: 0.7186 (p0) REVERT: A 331 ASP cc_start: 0.7223 (t0) cc_final: 0.6933 (t0) REVERT: A 338 LYS cc_start: 0.8881 (tptp) cc_final: 0.8641 (tptp) REVERT: A 340 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (tt) REVERT: A 341 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 450 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mmm) REVERT: A 451 VAL cc_start: 0.7985 (t) cc_final: 0.7767 (t) REVERT: A 509 GLN cc_start: 0.6205 (tp-100) cc_final: 0.5952 (tp-100) REVERT: A 705 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 721 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7460 (tpp) REVERT: A 761 TYR cc_start: 0.7461 (m-80) cc_final: 0.6954 (m-80) REVERT: C 48 LYS cc_start: 0.8322 (mttp) cc_final: 0.7939 (mttp) REVERT: C 70 LYS cc_start: 0.8315 (mttt) cc_final: 0.7913 (mttt) REVERT: C 156 ASP cc_start: 0.8332 (m-30) cc_final: 0.8015 (m-30) REVERT: C 157 ILE cc_start: 0.8541 (tp) cc_final: 0.8236 (tp) REVERT: C 161 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6574 (mpp) REVERT: C 192 ARG cc_start: 0.8428 (mtm180) cc_final: 0.8117 (mtm-85) REVERT: C 569 PHE cc_start: 0.7796 (t80) cc_final: 0.7357 (t80) REVERT: C 628 THR cc_start: 0.8059 (m) cc_final: 0.7758 (p) REVERT: C 634 LEU cc_start: 0.7724 (tt) cc_final: 0.7455 (tp) REVERT: C 679 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7984 (ttmt) REVERT: C 690 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6902 (mm) REVERT: C 693 VAL cc_start: 0.7948 (t) cc_final: 0.7330 (p) REVERT: C 705 ASP cc_start: 0.7568 (t0) cc_final: 0.6563 (t0) REVERT: C 793 LYS cc_start: 0.8358 (mttp) cc_final: 0.8141 (mttm) REVERT: C 802 CYS cc_start: 0.6961 (m) cc_final: 0.6303 (t) REVERT: E 222 ILE cc_start: 0.8305 (tp) cc_final: 0.8075 (tp) outliers start: 83 outliers final: 57 residues processed: 416 average time/residue: 0.2566 time to fit residues: 156.2710 Evaluate side-chains 424 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 360 time to evaluate : 1.609 ------------------------------------------------------------------------------- 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 88 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 268 LEU 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 450 MET Chi-restraints excluded: chain A residue 469 MET 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 721 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU 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 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 571 CYS 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 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 D residue 141 ILE Chi-restraints excluded: chain E residue 124 CYS Chi-restraints excluded: chain E residue 132 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 0.0770 chunk 57 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 100 optimal weight: 0.0270 chunk 189 optimal weight: 6.9990 chunk 136 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 chunk 186 optimal weight: 0.0270 chunk 30 optimal weight: 0.1980 chunk 191 optimal weight: 0.0670 overall best weight: 0.0490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN A 641 GLN A 700 HIS C 299 ASN C 663 GLN C 680 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132468 restraints weight = 30804.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.136680 restraints weight = 17260.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.139513 restraints weight = 10968.244| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15236 Z= 0.123 Angle : 0.678 15.725 20639 Z= 0.327 Chirality : 0.039 0.154 2512 Planarity : 0.004 0.059 2611 Dihedral : 4.199 21.570 2057 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.99 % Allowed : 29.20 % Favored : 66.81 % 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: -0.07 (0.20), residues: 1914 helix: 1.13 (0.16), residues: 1075 sheet: -0.77 (1.09), residues: 22 loop : -1.69 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 123 HIS 0.004 0.001 HIS C 173 PHE 0.026 0.001 PHE C 482 TYR 0.021 0.001 TYR A 99 ARG 0.008 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 729) hydrogen bonds : angle 4.34168 ( 2121) covalent geometry : bond 0.00269 (15236) covalent geometry : angle 0.67825 (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 435 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 371 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8521 (tttt) cc_final: 0.7804 (tptp) REVERT: A 139 TYR cc_start: 0.7545 (t80) cc_final: 0.7251 (t80) REVERT: A 235 GLN cc_start: 0.7053 (mp10) cc_final: 0.6665 (mp10) REVERT: A 290 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7834 (ttpp) REVERT: A 315 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6609 (mmmm) REVERT: A 324 ASN cc_start: 0.7894 (t0) cc_final: 0.7109 (p0) REVERT: A 331 ASP cc_start: 0.7235 (t0) cc_final: 0.6951 (t0) REVERT: A 338 LYS cc_start: 0.8903 (tptp) cc_final: 0.8668 (tptp) REVERT: A 341 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 377 TYR cc_start: 0.8349 (m-80) cc_final: 0.7772 (m-80) REVERT: A 419 PRO cc_start: 0.7747 (Cg_exo) cc_final: 0.7478 (Cg_endo) REVERT: A 451 VAL cc_start: 0.7895 (t) cc_final: 0.7694 (t) REVERT: A 509 GLN cc_start: 0.6114 (tp-100) cc_final: 0.5866 (tp-100) REVERT: A 606 PHE cc_start: 0.4760 (m-10) cc_final: 0.4397 (m-10) REVERT: A 705 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 721 MET cc_start: 0.7691 (tpp) cc_final: 0.7385 (tpp) REVERT: A 761 TYR cc_start: 0.7365 (m-80) cc_final: 0.6858 (m-80) REVERT: C 70 LYS cc_start: 0.8337 (mttt) cc_final: 0.7959 (mttt) REVERT: C 156 ASP cc_start: 0.8279 (m-30) cc_final: 0.8006 (m-30) REVERT: C 157 ILE cc_start: 0.8499 (tp) cc_final: 0.8217 (tp) REVERT: C 161 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: C 192 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7977 (mtm-85) REVERT: C 194 ARG cc_start: 0.7966 (mpt180) cc_final: 0.7250 (mmt-90) REVERT: C 221 GLU cc_start: 0.7980 (tp30) cc_final: 0.7597 (tp30) REVERT: C 494 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7535 (mttt) REVERT: C 628 THR cc_start: 0.7865 (m) cc_final: 0.7620 (p) REVERT: C 634 LEU cc_start: 0.7603 (tt) cc_final: 0.7352 (tp) REVERT: C 690 ILE cc_start: 0.7219 (mt) cc_final: 0.6766 (mm) REVERT: C 693 VAL cc_start: 0.7871 (t) cc_final: 0.7255 (p) REVERT: C 705 ASP cc_start: 0.7574 (t0) cc_final: 0.6532 (t0) REVERT: C 793 LYS cc_start: 0.8277 (mttp) cc_final: 0.7761 (mttm) REVERT: C 802 CYS cc_start: 0.6863 (m) cc_final: 0.6287 (t) REVERT: E 222 ILE cc_start: 0.8291 (tp) cc_final: 0.8060 (tp) outliers start: 64 outliers final: 42 residues processed: 404 average time/residue: 0.2723 time to fit residues: 160.6484 Evaluate side-chains 407 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN 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 290 LYS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET 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 633 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 96 LEU 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 232 ARG Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU 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 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 132 SER Chi-restraints excluded: chain E residue 142 LEU 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: 0.0570 chunk 188 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 97 optimal weight: 2.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN A 700 HIS C 299 ASN D 65 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 = 0.4187 r_free = 0.4187 target = 0.155298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.131048 restraints weight = 30552.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.135133 restraints weight = 17205.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137895 restraints weight = 11032.983| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3229 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= 0.123 Angle : 0.698 16.281 20639 Z= 0.335 Chirality : 0.039 0.182 2512 Planarity : 0.004 0.074 2611 Dihedral : 4.166 22.363 2057 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.31 % Allowed : 30.01 % Favored : 66.69 % 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: -0.09 (0.20), residues: 1914 helix: 1.07 (0.16), residues: 1076 sheet: -0.42 (1.08), residues: 22 loop : -1.64 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.002 0.001 HIS D 64 PHE 0.016 0.001 PHE A 251 TYR 0.018 0.001 TYR A 99 ARG 0.007 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 729) hydrogen bonds : angle 4.35470 ( 2121) covalent geometry : bond 0.00284 (15236) covalent geometry : angle 0.69790 (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 421 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 368 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8542 (tttt) cc_final: 0.7770 (tptp) REVERT: A 139 TYR cc_start: 0.7606 (t80) cc_final: 0.7308 (t80) REVERT: A 235 GLN cc_start: 0.7058 (mp10) cc_final: 0.6652 (mp10) REVERT: A 239 ASP cc_start: 0.7290 (t0) cc_final: 0.6956 (t0) REVERT: A 242 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7291 (ptt90) REVERT: A 290 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7848 (ttpp) REVERT: A 315 LYS cc_start: 0.7385 (mmtm) cc_final: 0.6746 (mmmm) REVERT: A 331 ASP cc_start: 0.7245 (t0) cc_final: 0.6961 (t0) REVERT: A 338 LYS cc_start: 0.8879 (tptp) cc_final: 0.8651 (tptp) REVERT: A 341 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 385 PHE cc_start: 0.7756 (m-80) cc_final: 0.7548 (m-80) REVERT: A 450 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7164 (mmm) REVERT: A 451 VAL cc_start: 0.7973 (t) cc_final: 0.7762 (t) REVERT: A 509 GLN cc_start: 0.6184 (tp-100) cc_final: 0.5861 (tp-100) REVERT: A 606 PHE cc_start: 0.5121 (m-10) cc_final: 0.4794 (m-10) REVERT: A 705 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 721 MET cc_start: 0.7710 (tpp) cc_final: 0.7406 (tpp) REVERT: A 761 TYR cc_start: 0.7385 (m-80) cc_final: 0.6895 (m-80) REVERT: C 70 LYS cc_start: 0.8328 (mttt) cc_final: 0.7967 (mttt) REVERT: C 156 ASP cc_start: 0.8287 (m-30) cc_final: 0.8019 (m-30) REVERT: C 157 ILE cc_start: 0.8505 (tp) cc_final: 0.8227 (tp) REVERT: C 161 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6583 (mpp) REVERT: C 173 HIS cc_start: 0.7649 (m-70) cc_final: 0.7209 (m-70) REVERT: C 192 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7998 (mtm-85) REVERT: C 194 ARG cc_start: 0.7924 (mpt180) cc_final: 0.7239 (mmt-90) REVERT: C 344 ASP cc_start: 0.7788 (t0) cc_final: 0.7509 (t0) REVERT: C 451 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7455 (mtt180) REVERT: C 494 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7544 (mttt) REVERT: C 628 THR cc_start: 0.7968 (m) cc_final: 0.7756 (p) REVERT: C 634 LEU cc_start: 0.7694 (tt) cc_final: 0.7422 (tp) REVERT: C 690 ILE cc_start: 0.7272 (mt) cc_final: 0.6828 (mm) REVERT: C 693 VAL cc_start: 0.7888 (t) cc_final: 0.7260 (p) REVERT: C 705 ASP cc_start: 0.7561 (t0) cc_final: 0.6520 (t0) REVERT: C 793 LYS cc_start: 0.8269 (mttp) cc_final: 0.7861 (mttm) REVERT: C 802 CYS cc_start: 0.6869 (m) cc_final: 0.6300 (t) REVERT: D 16 VAL cc_start: 0.7839 (t) cc_final: 0.7556 (t) REVERT: E 222 ILE cc_start: 0.8241 (tp) cc_final: 0.7993 (tp) outliers start: 53 outliers final: 44 residues processed: 393 average time/residue: 0.2649 time to fit residues: 151.8842 Evaluate side-chains 409 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 249 THR 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 311 LEU Chi-restraints excluded: chain A residue 426 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 41 LEU 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 172 PHE 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 306 THR Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 571 CYS Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 648 LEU 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 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 142 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 139 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 182 optimal weight: 0.4980 chunk 141 optimal weight: 4.9990 chunk 113 optimal weight: 0.0050 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS C 680 ASN D 65 HIS ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.155108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131087 restraints weight = 30631.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.135215 restraints weight = 17207.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.138005 restraints weight = 11010.201| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3363 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= 0.130 Angle : 0.711 16.755 20639 Z= 0.343 Chirality : 0.040 0.194 2512 Planarity : 0.004 0.076 2611 Dihedral : 4.218 22.758 2057 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.62 % Allowed : 29.76 % Favored : 66.63 % 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: -0.07 (0.20), residues: 1914 helix: 1.09 (0.16), residues: 1077 sheet: -0.03 (1.11), residues: 22 loop : -1.64 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.003 0.001 HIS A 304 PHE 0.025 0.001 PHE C 482 TYR 0.017 0.001 TYR A 99 ARG 0.007 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 729) hydrogen bonds : angle 4.40107 ( 2121) covalent geometry : bond 0.00302 (15236) covalent geometry : angle 0.71052 (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 427 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 369 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8552 (tttt) cc_final: 0.7847 (tptp) REVERT: A 139 TYR cc_start: 0.7598 (t80) cc_final: 0.7294 (t80) REVERT: A 235 GLN cc_start: 0.7067 (mp10) cc_final: 0.6667 (mp10) REVERT: A 242 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7374 (ptt90) REVERT: A 253 GLN cc_start: 0.7585 (mt0) cc_final: 0.7195 (mt0) REVERT: A 290 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7799 (ttpp) REVERT: A 315 LYS cc_start: 0.7400 (mmtm) cc_final: 0.7114 (mmmm) REVERT: A 324 ASN cc_start: 0.7926 (t0) cc_final: 0.7171 (p0) REVERT: A 331 ASP cc_start: 0.7242 (t0) cc_final: 0.6915 (t0) REVERT: A 338 LYS cc_start: 0.8900 (tptp) cc_final: 0.8681 (tptp) REVERT: A 341 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 419 PRO cc_start: 0.7792 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: A 450 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7158 (mmm) REVERT: A 503 LYS cc_start: 0.7637 (tptp) cc_final: 0.7274 (mtmm) REVERT: A 509 GLN cc_start: 0.6178 (tp-100) cc_final: 0.5943 (tp-100) REVERT: A 606 PHE cc_start: 0.4962 (m-10) cc_final: 0.4659 (m-10) REVERT: A 705 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7205 (mm-30) REVERT: A 721 MET cc_start: 0.7646 (tpp) cc_final: 0.7340 (tpp) REVERT: A 761 TYR cc_start: 0.7423 (m-80) cc_final: 0.7021 (m-80) REVERT: C 48 LYS cc_start: 0.8329 (mttp) cc_final: 0.7757 (mttm) REVERT: C 152 LEU cc_start: 0.8712 (mt) cc_final: 0.8437 (mt) REVERT: C 156 ASP cc_start: 0.8297 (m-30) cc_final: 0.7952 (m-30) REVERT: C 157 ILE cc_start: 0.8516 (tp) cc_final: 0.8239 (tp) REVERT: C 161 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: C 192 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7915 (mtm-85) REVERT: C 221 GLU cc_start: 0.8020 (tp30) cc_final: 0.7664 (tp30) REVERT: C 437 LYS cc_start: 0.7836 (ptpp) cc_final: 0.7421 (pttp) REVERT: C 441 LYS cc_start: 0.8592 (mptt) cc_final: 0.8357 (mmtm) REVERT: C 451 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7469 (mtt180) REVERT: C 494 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7594 (mttt) REVERT: C 569 PHE cc_start: 0.7652 (t80) cc_final: 0.7238 (t80) REVERT: C 593 MET cc_start: 0.8012 (tpp) cc_final: 0.7630 (tpp) REVERT: C 634 LEU cc_start: 0.7702 (tt) cc_final: 0.7414 (tp) REVERT: C 679 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8206 (mtmt) REVERT: C 690 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6870 (mm) REVERT: C 693 VAL cc_start: 0.7834 (t) cc_final: 0.7186 (p) REVERT: C 705 ASP cc_start: 0.7575 (t0) cc_final: 0.6481 (t0) REVERT: C 793 LYS cc_start: 0.8205 (mttp) cc_final: 0.7787 (mttp) REVERT: C 802 CYS cc_start: 0.6838 (m) cc_final: 0.6274 (t) REVERT: D 16 VAL cc_start: 0.7898 (t) cc_final: 0.7618 (t) REVERT: D 132 MET cc_start: 0.7127 (mpp) cc_final: 0.6913 (mpp) REVERT: E 222 ILE cc_start: 0.8258 (tp) cc_final: 0.7995 (tp) outliers start: 58 outliers final: 46 residues processed: 396 average time/residue: 0.2747 time to fit residues: 158.0807 Evaluate side-chains 411 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 242 ARG Chi-restraints excluded: chain A residue 249 THR 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 311 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 450 MET 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 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 95 MET Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 172 PHE 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 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 608 LEU Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 690 ILE 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 101 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain E residue 142 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 22 optimal weight: 0.0270 chunk 26 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 0.0980 chunk 148 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 700 HIS C 680 ASN D 65 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 = 0.4182 r_free = 0.4182 target = 0.155424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131731 restraints weight = 30143.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135893 restraints weight = 16907.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138673 restraints weight = 10750.338| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3475 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= 0.127 Angle : 0.710 17.227 20639 Z= 0.341 Chirality : 0.040 0.186 2512 Planarity : 0.004 0.076 2611 Dihedral : 4.217 22.797 2057 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.49 % Allowed : 30.19 % Favored : 66.31 % 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: -0.08 (0.20), residues: 1914 helix: 1.06 (0.16), residues: 1079 sheet: 0.15 (1.14), residues: 22 loop : -1.63 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 123 HIS 0.003 0.001 HIS D 64 PHE 0.016 0.001 PHE A 251 TYR 0.017 0.001 TYR A 99 ARG 0.007 0.001 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 729) hydrogen bonds : angle 4.39709 ( 2121) covalent geometry : bond 0.00296 (15236) covalent geometry : angle 0.71019 (20639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6548.38 seconds wall clock time: 114 minutes 30.16 seconds (6870.16 seconds total)