Starting phenix.real_space_refine on Thu Feb 13 22:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.map" model { file = "/net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eoj_28377/02_2025/8eoj_28377.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 35 5.16 5 C 5936 2.51 5 N 1574 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3326 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 6001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 781, 5996 Classifications: {'peptide': 781} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 761} Chain breaks: 9 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 781, 5996 Classifications: {'peptide': 781} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 761} Chain breaks: 9 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 6064 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 824 " occ=0.60 ... (8 atoms not shown) pdb=" CB BPHE B 824 " occ=0.40 Time building chain proxies: 8.81, per 1000 atoms: 0.94 Number of scatterers: 9327 At special positions: 0 Unit cell: (89.64, 100.44, 158.76, 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 35 16.00 O 1782 8.00 N 1574 7.00 C 5936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 827 " - pdb=" SG CYS B 878 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 37.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 53 through 73 Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.944A pdb=" N ALA A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.957A pdb=" N LYS A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.913A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.773A pdb=" N PHE A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.510A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.548A pdb=" N GLY A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.600A pdb=" N SER A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.570A pdb=" N PHE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 4.167A pdb=" N CYS A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 414 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.646A pdb=" N SER A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.673A pdb=" N LEU B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.533A pdb=" N LYS B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.209A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.501A pdb=" N THR B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.924A pdb=" N LEU B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 338 removed outlier: 3.507A pdb=" N VAL B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.668A pdb=" N ILE B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.575A pdb=" N LEU B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.815A pdb=" N GLN B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.522A pdb=" N GLU B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 485 through 494 Processing helix chain 'B' and resid 497 through 511 removed outlier: 3.549A pdb=" N TYR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 529 removed outlier: 3.611A pdb=" N ARG B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 550 Processing helix chain 'B' and resid 553 through 564 Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.763A pdb=" N TYR B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.592A pdb=" N PHE B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 879 removed outlier: 4.119A pdb=" N MET B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.996A pdb=" N GLU A 21 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 29 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 83 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 45 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 82 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU A 47 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 44 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 105 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 8.252A pdb=" N THR A 187 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A 159 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 206 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 158 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 160 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 202 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 removed outlier: 5.777A pdb=" N ILE A 238 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 257 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 318 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 316 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 317 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 319 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.883A pdb=" N LYS A 370 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ASP A 426 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 389 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET A 425 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 391 " --> pdb=" O MET A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 238 removed outlier: 3.893A pdb=" N ILE B 250 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 238 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 248 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS B 35 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 42 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR B 57 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 58 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 89 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 60 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 87 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 124 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE B 135 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS B 126 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 135 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 137 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 166 removed outlier: 9.491A pdb=" N ASN B 173 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP B 192 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS B 175 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 185 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 617 through 623 removed outlier: 6.238A pdb=" N THR B 618 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 633 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR B 620 " --> pdb=" O TYR B 631 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 631 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 622 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 644 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 652 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS B 660 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 654 " --> pdb=" O GLY B 658 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY B 658 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA B 690 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 728 through 737 removed outlier: 6.562A pdb=" N GLY B 755 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 736 " --> pdb=" O VAL B 753 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 753 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 728 through 737 removed outlier: 6.562A pdb=" N GLY B 755 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 736 " --> pdb=" O VAL B 753 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 753 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 748 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 754 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA B 758 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR B 783 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP B 760 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG B 781 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 804 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 840 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 808 " --> pdb=" O PRO B 836 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 835 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 855 " --> pdb=" O LYS B 843 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 763 through 764 removed outlier: 3.879A pdb=" N ALA B 764 " --> pdb=" O ARG B 777 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET B 830 " --> pdb=" O PHE B 868 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1167 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: 3.11 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3037 1.34 - 1.46: 1959 1.46 - 1.58: 4424 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 9474 Sorted by residual: bond pdb=" CA LYS B 299 " pdb=" C LYS B 299 " ideal model delta sigma weight residual 1.529 1.513 0.017 9.30e-03 1.16e+04 3.19e+00 bond pdb=" C LEU B 870 " pdb=" O LEU B 870 " ideal model delta sigma weight residual 1.243 1.230 0.013 9.50e-03 1.11e+04 1.98e+00 bond pdb=" N PRO A 441 " pdb=" CA PRO A 441 " ideal model delta sigma weight residual 1.469 1.478 -0.010 7.40e-03 1.83e+04 1.66e+00 bond pdb=" C LEU B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.63e+00 bond pdb=" C ILE B 486 " pdb=" N PRO B 487 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.47e+00 ... (remaining 9469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12571 1.75 - 3.49: 166 3.49 - 5.24: 27 5.24 - 6.98: 15 6.98 - 8.73: 1 Bond angle restraints: 12780 Sorted by residual: angle pdb=" C LEU B 870 " pdb=" CA LEU B 870 " pdb=" CB LEU B 870 " ideal model delta sigma weight residual 117.23 110.90 6.33 1.36e+00 5.41e-01 2.17e+01 angle pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" C THR A 110 " ideal model delta sigma weight residual 110.80 119.53 -8.73 2.13e+00 2.20e-01 1.68e+01 angle pdb=" C ARG A 30 " pdb=" N LYS A 31 " pdb=" CA LYS A 31 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CA LYS B 299 " pdb=" C LYS B 299 " pdb=" N GLY B 300 " ideal model delta sigma weight residual 119.52 116.81 2.71 7.90e-01 1.60e+00 1.18e+01 angle pdb=" C TYR B 138 " pdb=" N GLN B 139 " pdb=" CA GLN B 139 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 12775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5407 17.39 - 34.79: 273 34.79 - 52.18: 75 52.18 - 69.58: 6 69.58 - 86.97: 2 Dihedral angle restraints: 5763 sinusoidal: 2234 harmonic: 3529 Sorted by residual: dihedral pdb=" CB CYS B 298 " pdb=" SG CYS B 298 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -166.60 80.60 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CA ASP A 451 " pdb=" C ASP A 451 " pdb=" N ARG A 452 " pdb=" CA ARG A 452 " ideal model delta harmonic sigma weight residual 180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU B 741 " pdb=" C LEU B 741 " pdb=" N GLN B 742 " pdb=" CA GLN B 742 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1046 0.037 - 0.073: 294 0.073 - 0.110: 102 0.110 - 0.147: 39 0.147 - 0.184: 1 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PHE A 440 " pdb=" N PHE A 440 " pdb=" C PHE A 440 " pdb=" CB PHE A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1479 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 99 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO A 100 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 567 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 568 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 568 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 568 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 440 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 441 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.023 5.00e-02 4.00e+02 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 918 2.75 - 3.29: 8798 3.29 - 3.83: 15426 3.83 - 4.36: 17538 4.36 - 4.90: 30571 Nonbonded interactions: 73251 Sorted by model distance: nonbonded pdb=" OH TYR A 116 " pdb=" O GLY A 119 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLU B 167 " pdb=" OH TYR B 178 " model vdw 2.261 3.040 nonbonded pdb=" O ILE B 560 " pdb=" OG SER B 563 " model vdw 2.277 3.040 nonbonded pdb=" O ALA A 336 " pdb=" OG1 THR A 340 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASP A 83 " pdb=" OG1 THR A 85 " model vdw 2.307 3.040 ... (remaining 73246 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 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 : 0.002 0.034 9474 Z= 0.159 Angle : 0.555 8.731 12780 Z= 0.308 Chirality : 0.042 0.184 1482 Planarity : 0.004 0.049 1629 Dihedral : 11.261 86.970 3461 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.76 % Allowed : 7.92 % Favored : 88.32 % 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: -1.48 (0.22), residues: 1186 helix: -0.69 (0.22), residues: 411 sheet: -0.40 (0.33), residues: 274 loop : -1.44 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 396 HIS 0.003 0.001 HIS B 529 PHE 0.014 0.001 PHE A 209 TYR 0.008 0.001 TYR B 620 ARG 0.001 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.6536 (tt0) cc_final: 0.6153 (tp30) REVERT: A 92 GLN cc_start: 0.1837 (tt0) cc_final: 0.1136 (pp30) REVERT: A 154 GLU cc_start: 0.7191 (tp30) cc_final: 0.6891 (tp30) REVERT: A 216 PHE cc_start: 0.6288 (t80) cc_final: 0.6017 (t80) REVERT: A 229 ILE cc_start: 0.5436 (OUTLIER) cc_final: 0.5110 (mt) REVERT: A 316 ARG cc_start: 0.4856 (mmt-90) cc_final: 0.4378 (tpp-160) REVERT: A 322 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6911 (tm-30) REVERT: A 376 ASN cc_start: 0.8043 (m-40) cc_final: 0.7734 (m110) REVERT: A 412 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5812 (mp0) REVERT: B 262 GLU cc_start: 0.6156 (mt-10) cc_final: 0.5950 (mt-10) REVERT: B 277 ILE cc_start: 0.5637 (OUTLIER) cc_final: 0.5339 (mp) REVERT: B 343 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7453 (tm-30) REVERT: B 491 LYS cc_start: 0.8654 (tttm) cc_final: 0.8238 (ttpp) REVERT: B 551 ASN cc_start: 0.6391 (t0) cc_final: 0.6032 (t0) REVERT: B 555 MET cc_start: 0.8492 (mmm) cc_final: 0.8118 (mmm) REVERT: B 777 ARG cc_start: 0.7810 (ptp90) cc_final: 0.6938 (mmt180) outliers start: 37 outliers final: 11 residues processed: 265 average time/residue: 0.2565 time to fit residues: 90.4372 Evaluate side-chains 179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 430 ASN B 93 ASN B 502 HIS ** B 754 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 = 0.4747 r_free = 0.4747 target = 0.179694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.164406 restraints weight = 25988.110| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 3.55 r_work: 0.4451 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4452 r_free = 0.4452 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4452 r_free = 0.4452 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9474 Z= 0.225 Angle : 0.657 14.200 12780 Z= 0.329 Chirality : 0.046 0.225 1482 Planarity : 0.004 0.040 1629 Dihedral : 5.954 54.473 1305 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.35 % Allowed : 14.21 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1186 helix: 0.29 (0.24), residues: 422 sheet: -0.22 (0.33), residues: 271 loop : -1.32 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 128 HIS 0.008 0.001 HIS B 502 PHE 0.019 0.002 PHE B 840 TYR 0.015 0.002 TYR A 268 ARG 0.006 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.2291 (tt0) cc_final: 0.1158 (pp30) REVERT: A 181 ASP cc_start: 0.6924 (p0) cc_final: 0.6657 (p0) REVERT: A 216 PHE cc_start: 0.6557 (t80) cc_final: 0.6283 (t80) REVERT: A 322 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7097 (tm-30) REVERT: A 376 ASN cc_start: 0.8073 (m-40) cc_final: 0.7760 (m110) REVERT: A 408 ASP cc_start: 0.1363 (m-30) cc_final: 0.1037 (m-30) REVERT: B 170 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5594 (tp) REVERT: B 551 ASN cc_start: 0.6503 (t0) cc_final: 0.6282 (t0) REVERT: B 777 ARG cc_start: 0.7403 (ptp90) cc_final: 0.7088 (mmt180) REVERT: B 877 MET cc_start: -0.0061 (OUTLIER) cc_final: -0.0336 (tpt) outliers start: 33 outliers final: 14 residues processed: 201 average time/residue: 0.2420 time to fit residues: 65.4184 Evaluate side-chains 171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 877 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 7 optimal weight: 0.0000 chunk 45 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 256 HIS A 298 ASN ** B 754 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 = 0.4761 r_free = 0.4761 target = 0.180468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.165301 restraints weight = 25998.576| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 3.59 r_work: 0.4468 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9474 Z= 0.180 Angle : 0.596 12.526 12780 Z= 0.301 Chirality : 0.044 0.167 1482 Planarity : 0.004 0.045 1629 Dihedral : 5.119 47.321 1293 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 3.65 % Allowed : 15.74 % Favored : 80.61 % 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: -0.51 (0.24), residues: 1186 helix: 0.64 (0.25), residues: 422 sheet: -0.19 (0.33), residues: 271 loop : -1.23 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 128 HIS 0.004 0.001 HIS B 335 PHE 0.019 0.002 PHE A 282 TYR 0.012 0.001 TYR A 196 ARG 0.003 0.000 ARG B 623 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLN cc_start: 0.2551 (tt0) cc_final: 0.1701 (pp30) REVERT: A 97 ARG cc_start: 0.6155 (mmt180) cc_final: 0.5925 (mmt180) REVERT: A 216 PHE cc_start: 0.6408 (t80) cc_final: 0.6091 (t80) REVERT: A 299 GLN cc_start: 0.6833 (tp-100) cc_final: 0.6012 (mt0) REVERT: A 322 GLU cc_start: 0.7432 (tm-30) cc_final: 0.6973 (tm-30) REVERT: A 376 ASN cc_start: 0.8084 (m-40) cc_final: 0.7858 (m110) REVERT: A 408 ASP cc_start: 0.1345 (m-30) cc_final: 0.0840 (t70) REVERT: B 268 MET cc_start: 0.5021 (mtt) cc_final: 0.4184 (ptp) REVERT: B 277 ILE cc_start: 0.5691 (OUTLIER) cc_final: 0.5316 (mp) REVERT: B 551 ASN cc_start: 0.6658 (t0) cc_final: 0.6400 (t0) REVERT: B 877 MET cc_start: 0.0500 (OUTLIER) cc_final: 0.0277 (tpt) outliers start: 36 outliers final: 21 residues processed: 185 average time/residue: 0.2569 time to fit residues: 64.1516 Evaluate side-chains 163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 877 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN B 390 GLN B 737 HIS ** B 754 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 = 0.4719 r_free = 0.4719 target = 0.177445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.162420 restraints weight = 26038.735| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 3.49 r_work: 0.4425 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9474 Z= 0.289 Angle : 0.670 12.050 12780 Z= 0.341 Chirality : 0.046 0.183 1482 Planarity : 0.005 0.104 1629 Dihedral : 5.597 47.588 1293 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.47 % Allowed : 14.92 % Favored : 80.61 % 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: -0.72 (0.24), residues: 1186 helix: 0.50 (0.25), residues: 421 sheet: -0.32 (0.32), residues: 267 loop : -1.37 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 128 HIS 0.007 0.001 HIS B 335 PHE 0.015 0.002 PHE B 608 TYR 0.014 0.002 TYR A 196 ARG 0.010 0.001 ARG B 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7131 (ptpp) cc_final: 0.6782 (ptpp) REVERT: A 87 GLU cc_start: 0.7699 (mp0) cc_final: 0.7289 (mp0) REVERT: A 97 ARG cc_start: 0.6202 (mmt180) cc_final: 0.5917 (mmt180) REVERT: A 216 PHE cc_start: 0.6434 (t80) cc_final: 0.6137 (t80) REVERT: A 299 GLN cc_start: 0.6546 (tp-100) cc_final: 0.6308 (tp-100) REVERT: A 322 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7009 (tm-30) REVERT: A 324 MET cc_start: 0.4769 (mmt) cc_final: 0.4524 (mmt) REVERT: A 376 ASN cc_start: 0.8085 (m-40) cc_final: 0.7851 (m110) REVERT: A 412 GLU cc_start: 0.5095 (OUTLIER) cc_final: 0.4826 (mp0) REVERT: B 277 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5394 (mp) REVERT: B 551 ASN cc_start: 0.6622 (t0) cc_final: 0.6352 (t0) outliers start: 44 outliers final: 28 residues processed: 186 average time/residue: 0.2403 time to fit residues: 60.5732 Evaluate side-chains 177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 76 optimal weight: 0.8980 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.182643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.167645 restraints weight = 25720.233| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 3.52 r_work: 0.4491 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9474 Z= 0.155 Angle : 0.576 11.994 12780 Z= 0.288 Chirality : 0.043 0.167 1482 Planarity : 0.004 0.065 1629 Dihedral : 5.000 46.712 1293 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 17.46 % Favored : 79.59 % 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: -0.47 (0.24), residues: 1186 helix: 0.89 (0.25), residues: 421 sheet: -0.30 (0.32), residues: 276 loop : -1.35 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 396 HIS 0.002 0.001 HIS B 335 PHE 0.019 0.001 PHE A 282 TYR 0.018 0.001 TYR B 511 ARG 0.003 0.000 ARG B 777 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.6980 (ptpp) cc_final: 0.6555 (ptpp) REVERT: A 93 GLN cc_start: 0.3512 (tp40) cc_final: 0.3160 (tp-100) REVERT: A 162 LYS cc_start: 0.6365 (mttt) cc_final: 0.4324 (pttt) REVERT: A 216 PHE cc_start: 0.6452 (t80) cc_final: 0.6129 (t80) REVERT: A 303 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8453 (mm-30) REVERT: A 322 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 412 GLU cc_start: 0.4813 (OUTLIER) cc_final: 0.4498 (mp0) REVERT: B 53 ASP cc_start: 0.4652 (OUTLIER) cc_final: 0.4413 (m-30) outliers start: 29 outliers final: 22 residues processed: 180 average time/residue: 0.2352 time to fit residues: 57.9991 Evaluate side-chains 176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 32 optimal weight: 0.0000 chunk 86 optimal weight: 0.6980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.182067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.167040 restraints weight = 25593.286| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 3.54 r_work: 0.4485 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4490 r_free = 0.4490 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4490 r_free = 0.4490 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9474 Z= 0.164 Angle : 0.573 11.626 12780 Z= 0.287 Chirality : 0.043 0.151 1482 Planarity : 0.004 0.051 1629 Dihedral : 4.861 45.267 1291 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.25 % Allowed : 18.58 % Favored : 78.17 % 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: -0.40 (0.24), residues: 1186 helix: 0.94 (0.25), residues: 426 sheet: -0.07 (0.33), residues: 270 loop : -1.44 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.004 0.001 HIS B 603 PHE 0.016 0.002 PHE A 282 TYR 0.018 0.002 TYR B 511 ARG 0.003 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7023 (ptpp) cc_final: 0.6502 (ptpp) REVERT: A 87 GLU cc_start: 0.7578 (mp0) cc_final: 0.7349 (mp0) REVERT: A 93 GLN cc_start: 0.3466 (tp40) cc_final: 0.3041 (tp-100) REVERT: A 97 ARG cc_start: 0.5980 (mpt180) cc_final: 0.5616 (mmt180) REVERT: A 216 PHE cc_start: 0.6580 (t80) cc_final: 0.6244 (t80) REVERT: A 322 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6765 (tm-30) REVERT: A 412 GLU cc_start: 0.4839 (OUTLIER) cc_final: 0.4523 (mp0) outliers start: 32 outliers final: 22 residues processed: 179 average time/residue: 0.2345 time to fit residues: 57.4135 Evaluate side-chains 168 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 118 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.178603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.163485 restraints weight = 26266.143| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 3.57 r_work: 0.4449 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4454 r_free = 0.4454 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4454 r_free = 0.4454 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9474 Z= 0.218 Angle : 0.622 11.462 12780 Z= 0.314 Chirality : 0.044 0.181 1482 Planarity : 0.004 0.050 1629 Dihedral : 5.140 43.385 1291 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.35 % Allowed : 18.27 % Favored : 78.38 % 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: -0.46 (0.24), residues: 1186 helix: 0.97 (0.25), residues: 419 sheet: -0.09 (0.33), residues: 270 loop : -1.53 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.005 0.001 HIS B 335 PHE 0.018 0.002 PHE B 706 TYR 0.032 0.002 TYR A 268 ARG 0.003 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7735 (mp0) cc_final: 0.7428 (mp0) REVERT: A 93 GLN cc_start: 0.3614 (tp40) cc_final: 0.3203 (tp-100) REVERT: A 268 TYR cc_start: 0.5000 (OUTLIER) cc_final: 0.1990 (t80) REVERT: A 322 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6890 (tm-30) REVERT: A 412 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4594 (mp0) REVERT: B 268 MET cc_start: 0.4758 (mtt) cc_final: 0.3793 (mpp) REVERT: B 551 ASN cc_start: 0.7035 (t0) cc_final: 0.6717 (t0) outliers start: 33 outliers final: 26 residues processed: 169 average time/residue: 0.2410 time to fit residues: 55.8831 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.180571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.165346 restraints weight = 26505.460| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 3.67 r_work: 0.4460 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9474 Z= 0.186 Angle : 0.603 11.454 12780 Z= 0.304 Chirality : 0.044 0.173 1482 Planarity : 0.004 0.046 1629 Dihedral : 5.060 44.138 1291 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.15 % Allowed : 18.88 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1186 helix: 1.04 (0.26), residues: 418 sheet: 0.05 (0.34), residues: 268 loop : -1.52 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 396 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.002 PHE A 48 TYR 0.025 0.002 TYR A 268 ARG 0.002 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7693 (mp0) cc_final: 0.7411 (mp0) REVERT: A 93 GLN cc_start: 0.3289 (tp40) cc_final: 0.2940 (tp-100) REVERT: A 94 TYR cc_start: 0.3205 (m-10) cc_final: 0.2952 (m-10) REVERT: A 97 ARG cc_start: 0.5924 (mpt180) cc_final: 0.5647 (mmt180) REVERT: A 151 GLU cc_start: 0.4862 (OUTLIER) cc_final: 0.4642 (mp0) REVERT: A 162 LYS cc_start: 0.6293 (mttt) cc_final: 0.4263 (pttt) REVERT: A 216 PHE cc_start: 0.6646 (t80) cc_final: 0.6362 (t80) REVERT: A 233 GLN cc_start: 0.4953 (mm110) cc_final: 0.4714 (mm110) REVERT: A 268 TYR cc_start: 0.5064 (OUTLIER) cc_final: 0.2182 (t80) REVERT: A 299 GLN cc_start: 0.6745 (tp-100) cc_final: 0.6185 (mt0) REVERT: A 378 GLU cc_start: 0.8198 (mp0) cc_final: 0.7997 (mp0) REVERT: A 412 GLU cc_start: 0.4856 (OUTLIER) cc_final: 0.4561 (mp0) REVERT: B 268 MET cc_start: 0.4517 (mtt) cc_final: 0.3778 (mpp) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.2569 time to fit residues: 56.0308 Evaluate side-chains 168 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.178724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.163751 restraints weight = 25962.644| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 3.52 r_work: 0.4462 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4463 r_free = 0.4463 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9474 Z= 0.196 Angle : 0.615 11.388 12780 Z= 0.309 Chirality : 0.044 0.170 1482 Planarity : 0.004 0.047 1629 Dihedral : 5.070 43.540 1291 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.05 % Allowed : 18.78 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1186 helix: 1.06 (0.26), residues: 418 sheet: 0.12 (0.34), residues: 261 loop : -1.56 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 396 HIS 0.005 0.001 HIS B 335 PHE 0.022 0.002 PHE B 706 TYR 0.023 0.002 TYR A 268 ARG 0.006 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7666 (mp0) cc_final: 0.7397 (mp0) REVERT: A 93 GLN cc_start: 0.3323 (tp40) cc_final: 0.2971 (tp-100) REVERT: A 94 TYR cc_start: 0.3437 (m-10) cc_final: 0.3125 (m-10) REVERT: A 151 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.3904 (mp0) REVERT: A 162 LYS cc_start: 0.6322 (mttt) cc_final: 0.4268 (pttt) REVERT: A 216 PHE cc_start: 0.6665 (t80) cc_final: 0.6392 (t80) REVERT: A 299 GLN cc_start: 0.6605 (tp-100) cc_final: 0.6105 (mt0) REVERT: A 412 GLU cc_start: 0.4810 (OUTLIER) cc_final: 0.4502 (mp0) REVERT: B 268 MET cc_start: 0.4641 (mtt) cc_final: 0.3806 (mpp) outliers start: 30 outliers final: 26 residues processed: 161 average time/residue: 0.2305 time to fit residues: 50.9212 Evaluate side-chains 165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 827 CYS Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 0.0050 overall best weight: 0.3230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.182843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.167775 restraints weight = 26288.217| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 3.65 r_work: 0.4497 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6077 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9474 Z= 0.164 Angle : 0.615 12.514 12780 Z= 0.304 Chirality : 0.044 0.152 1482 Planarity : 0.004 0.048 1629 Dihedral : 4.888 45.597 1291 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.84 % Allowed : 19.39 % Favored : 77.77 % 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 (0.25), residues: 1186 helix: 1.21 (0.26), residues: 417 sheet: 0.20 (0.34), residues: 263 loop : -1.51 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 396 HIS 0.003 0.001 HIS B 335 PHE 0.022 0.001 PHE B 706 TYR 0.021 0.002 TYR A 268 ARG 0.008 0.000 ARG B 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7604 (mp0) cc_final: 0.7320 (mp0) REVERT: A 93 GLN cc_start: 0.3128 (tp40) cc_final: 0.2774 (tp-100) REVERT: A 151 GLU cc_start: 0.4798 (OUTLIER) cc_final: 0.3888 (mp0) REVERT: A 162 LYS cc_start: 0.6264 (mttt) cc_final: 0.4329 (pttt) REVERT: A 216 PHE cc_start: 0.6650 (t80) cc_final: 0.6405 (t80) REVERT: A 268 TYR cc_start: 0.4812 (OUTLIER) cc_final: 0.1936 (t80) REVERT: A 299 GLN cc_start: 0.6613 (tp-100) cc_final: 0.6196 (mt0) REVERT: A 412 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.4138 (mp0) REVERT: B 268 MET cc_start: 0.4644 (mtt) cc_final: 0.3923 (mpp) outliers start: 28 outliers final: 22 residues processed: 164 average time/residue: 0.2392 time to fit residues: 53.4428 Evaluate side-chains 165 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 627 SER Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 790 ILE Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 45 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.181567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.166375 restraints weight = 25976.526| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 3.59 r_work: 0.4469 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4474 r_free = 0.4474 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4474 r_free = 0.4474 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9474 Z= 0.186 Angle : 0.621 11.256 12780 Z= 0.311 Chirality : 0.044 0.185 1482 Planarity : 0.004 0.049 1629 Dihedral : 4.830 44.715 1289 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.34 % Allowed : 19.90 % Favored : 77.77 % 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 (0.25), residues: 1186 helix: 1.22 (0.26), residues: 417 sheet: 0.18 (0.34), residues: 261 loop : -1.50 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 396 HIS 0.016 0.001 HIS A 231 PHE 0.027 0.002 PHE B 706 TYR 0.021 0.002 TYR A 268 ARG 0.010 0.001 ARG B 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5451.20 seconds wall clock time: 97 minutes 28.14 seconds (5848.14 seconds total)