Starting phenix.real_space_refine on Sun Aug 24 12:26:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.map" model { file = "/net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jec_36185/08_2025/8jec_36185.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.066 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 84 5.16 5 C 12822 2.51 5 N 3332 2.21 5 O 3442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 653, 4847 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 19, 'TRANS': 633} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ASN:plan1': 9, 'ARG:plan': 11, 'TYR:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 5, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 258 Conformer: "B" Number of residues, atoms: 653, 4847 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 19, 'TRANS': 633} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ASN:plan1': 9, 'ARG:plan': 11, 'TYR:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 5, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 258 bond proxies already assigned to first conformer: 4940 Chain: "B" Number of atoms: 4984 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 663, 4975 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 19, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 15, 'ASN:plan1': 9, 'ARG:plan': 6, 'GLU:plan': 20, 'TYR:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 Conformer: "B" Number of residues, atoms: 663, 4975 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 19, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 15, 'ASN:plan1': 9, 'ARG:plan': 6, 'GLU:plan': 20, 'TYR:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 bond proxies already assigned to first conformer: 5071 Chain: "C" Number of atoms: 4856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 653, 4847 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 19, 'TRANS': 633} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ASN:plan1': 9, 'ARG:plan': 11, 'TYR:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 5, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 258 Conformer: "B" Number of residues, atoms: 653, 4847 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 19, 'TRANS': 633} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 437 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 13, 'ASN:plan1': 9, 'ARG:plan': 11, 'TYR:plan': 4, 'GLU:plan': 16, 'GLN:plan1': 5, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 258 bond proxies already assigned to first conformer: 4940 Chain: "D" Number of atoms: 4984 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 663, 4975 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 19, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 15, 'ASN:plan1': 9, 'ARG:plan': 6, 'GLU:plan': 20, 'TYR:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 Conformer: "B" Number of residues, atoms: 663, 4975 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 19, 'TRANS': 643} Chain breaks: 1 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 474 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 15, 'ASN:plan1': 9, 'ARG:plan': 6, 'GLU:plan': 20, 'TYR:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 bond proxies already assigned to first conformer: 5071 Time building chain proxies: 9.76, per 1000 atoms: 0.50 Number of scatterers: 19680 At special positions: 0 Unit cell: (102.01, 97.97, 181.8, 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 84 16.00 O 3442 8.00 N 3332 7.00 C 12822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4972 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 68.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 81 through 107 removed outlier: 4.366A pdb=" N MET A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 101 - end of helix Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 132 removed outlier: 3.587A pdb=" N ASP A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.790A pdb=" N LYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.610A pdb=" N ILE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 213 through 243 removed outlier: 4.378A pdb=" N LYS A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.615A pdb=" N GLU A 248 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 removed outlier: 3.534A pdb=" N THR A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 329 removed outlier: 3.941A pdb=" N ILE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 353 through 371 removed outlier: 3.656A pdb=" N GLY A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.501A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.673A pdb=" N LYS A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.617A pdb=" N GLN A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.791A pdb=" N ILE A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.823A pdb=" N LEU A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.606A pdb=" N PHE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 551 " --> pdb=" O GLU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.852A pdb=" N SER A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 593 through 603 removed outlier: 3.794A pdb=" N LEU A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 625 removed outlier: 3.720A pdb=" N ALA A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 3.600A pdb=" N LEU A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.930A pdb=" N VAL A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 699 removed outlier: 3.569A pdb=" N ILE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 722 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'B' and resid 79 through 106 removed outlier: 3.811A pdb=" N ILE B 91 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Proline residue: B 101 - end of helix Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 132 Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.512A pdb=" N ALA B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 removed outlier: 3.589A pdb=" N LEU B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.714A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 175 " --> pdb=" O TRP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.645A pdb=" N LEU B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 191 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 207 Processing helix chain 'B' and resid 212 through 243 removed outlier: 3.842A pdb=" N CYS B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 240 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.673A pdb=" N GLU B 248 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 250 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 287 removed outlier: 3.884A pdb=" N SER B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 329 removed outlier: 3.799A pdb=" N ILE B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 355 through 370 removed outlier: 3.566A pdb=" N LEU B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.694A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.644A pdb=" N ARG B 405 " --> pdb=" O PRO B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.583A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 417 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.525A pdb=" N CYS B 478 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 509 removed outlier: 3.645A pdb=" N ASN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 removed outlier: 4.180A pdb=" N ARG B 515 " --> pdb=" O HIS B 511 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 516 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 533 through 558 removed outlier: 3.727A pdb=" N ALA B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.547A pdb=" N LEU B 564 " --> pdb=" O ASP B 560 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.926A pdb=" N ARG B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 603 removed outlier: 4.073A pdb=" N TYR B 599 " --> pdb=" O ASP B 595 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 626 through 636 removed outlier: 3.964A pdb=" N ALA B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 656 removed outlier: 3.628A pdb=" N VAL B 652 " --> pdb=" O PHE B 648 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 654 " --> pdb=" O CYS B 650 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 655 " --> pdb=" O THR B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 680 through 689 removed outlier: 3.606A pdb=" N VAL B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 713 through 722 Processing helix chain 'B' and resid 723 through 740 removed outlier: 4.070A pdb=" N LEU B 729 " --> pdb=" O MET B 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 107 removed outlier: 4.385A pdb=" N MET C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP C 92 " --> pdb=" O PHE C 88 " (cutoff:3.500A) Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.590A pdb=" N ASP C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 150 through 169 removed outlier: 3.780A pdb=" N LYS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.604A pdb=" N ILE C 174 " --> pdb=" O PRO C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 212 through 243 removed outlier: 4.386A pdb=" N LYS C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.609A pdb=" N GLU C 248 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.530A pdb=" N THR C 277 " --> pdb=" O THR C 273 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 329 removed outlier: 3.930A pdb=" N ILE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 350 removed outlier: 3.518A pdb=" N ASN C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 371 removed outlier: 3.621A pdb=" N GLY C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.726A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 400 removed outlier: 3.700A pdb=" N LYS C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 408 through 417 removed outlier: 3.566A pdb=" N GLN C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.942A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C 479 " --> pdb=" O SER C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 509 Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.931A pdb=" N LEU C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 559 removed outlier: 3.674A pdb=" N THR C 538 " --> pdb=" O GLU C 534 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 542 " --> pdb=" O THR C 538 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS C 543 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 545 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 549 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 551 " --> pdb=" O GLU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 removed outlier: 3.654A pdb=" N SER C 566 " --> pdb=" O TYR C 562 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 Processing helix chain 'C' and resid 593 through 601 removed outlier: 3.655A pdb=" N THR C 597 " --> pdb=" O TYR C 593 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 600 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 601 " --> pdb=" O THR C 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 593 through 601' Processing helix chain 'C' and resid 616 through 624 removed outlier: 3.569A pdb=" N ALA C 621 " --> pdb=" O PRO C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.901A pdb=" N LEU C 632 " --> pdb=" O ARG C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 656 removed outlier: 3.773A pdb=" N CYS C 650 " --> pdb=" O GLY C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 666 Processing helix chain 'C' and resid 680 through 689 removed outlier: 4.104A pdb=" N VAL C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 700 removed outlier: 3.892A pdb=" N GLN C 696 " --> pdb=" O VAL C 692 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 697 " --> pdb=" O LEU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 722 Processing helix chain 'C' and resid 723 through 740 Processing helix chain 'D' and resid 79 through 106 removed outlier: 3.823A pdb=" N ILE D 91 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP D 92 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 114 through 132 Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.596A pdb=" N ALA D 153 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 169 removed outlier: 3.587A pdb=" N LEU D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.716A pdb=" N ILE D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.646A pdb=" N LEU D 187 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG D 191 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 207 Processing helix chain 'D' and resid 212 through 243 removed outlier: 3.552A pdb=" N TYR D 238 " --> pdb=" O CYS D 234 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.674A pdb=" N GLU D 248 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY D 249 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 250 " --> pdb=" O GLN D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 287 removed outlier: 3.890A pdb=" N SER D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 330 removed outlier: 3.801A pdb=" N ILE D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 Processing helix chain 'D' and resid 355 through 370 removed outlier: 3.666A pdb=" N GLN D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 398 Processing helix chain 'D' and resid 401 through 405 removed outlier: 3.683A pdb=" N ARG D 405 " --> pdb=" O PRO D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 418 removed outlier: 3.539A pdb=" N ILE D 415 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 417 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.563A pdb=" N ILE D 476 " --> pdb=" O GLY D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 509 removed outlier: 3.555A pdb=" N MET D 503 " --> pdb=" O LYS D 499 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN D 504 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 522 removed outlier: 4.159A pdb=" N ARG D 515 " --> pdb=" O HIS D 511 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU D 517 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 533 through 558 removed outlier: 3.658A pdb=" N ALA D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.964A pdb=" N ARG D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 removed outlier: 3.860A pdb=" N ARG D 591 " --> pdb=" O LEU D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 603 removed outlier: 3.652A pdb=" N TYR D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 624 Processing helix chain 'D' and resid 626 through 636 removed outlier: 3.881A pdb=" N ALA D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 656 removed outlier: 4.806A pdb=" N VAL D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA D 654 " --> pdb=" O CYS D 650 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS D 655 " --> pdb=" O THR D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 667 removed outlier: 3.565A pdb=" N ARG D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 664 " --> pdb=" O PHE D 660 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER D 666 " --> pdb=" O LYS D 662 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN D 667 " --> pdb=" O ARG D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 removed outlier: 3.620A pdb=" N VAL D 684 " --> pdb=" O THR D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 700 Processing helix chain 'D' and resid 713 through 722 Processing helix chain 'D' and resid 723 through 740 removed outlier: 4.008A pdb=" N LEU D 729 " --> pdb=" O MET D 725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 424 removed outlier: 3.594A pdb=" N CYS A 492 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 441 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 463 through 465 removed outlier: 4.088A pdb=" N ALA A 463 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 448 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 420 through 424 removed outlier: 3.588A pdb=" N TYR B 441 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 429 through 431 removed outlier: 6.462A pdb=" N VAL B 429 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 488 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 431 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 463 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY B 452 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE B 461 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 420 through 424 removed outlier: 3.554A pdb=" N CYS C 492 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS C 469 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 463 through 465 removed outlier: 4.142A pdb=" N ALA C 463 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 448 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424 removed outlier: 3.556A pdb=" N TYR D 441 " --> pdb=" O PHE D 471 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 429 through 431 removed outlier: 6.414A pdb=" N VAL D 429 " --> pdb=" O VAL D 488 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 488 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET D 431 " --> pdb=" O VAL D 486 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA D 463 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY D 452 " --> pdb=" O ILE D 461 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE D 461 " --> pdb=" O GLY D 452 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3231 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: 3.54 Time building geometry restraints manager: 2.25 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: 6304 1.34 - 1.46: 4570 1.46 - 1.58: 9096 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 20110 Sorted by residual: bond pdb=" C LEU D 395 " pdb=" N PRO D 396 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.08e-02 8.57e+03 2.26e+00 bond pdb=" C LEU B 395 " pdb=" N PRO B 396 " ideal model delta sigma weight residual 1.337 1.351 -0.015 9.80e-03 1.04e+04 2.20e+00 bond pdb=" C GLY D 722 " pdb=" O GLY D 722 " ideal model delta sigma weight residual 1.236 1.230 0.006 5.30e-03 3.56e+04 1.18e+00 bond pdb=" N GLU D 268 " pdb=" CA GLU D 268 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.24e-01 bond pdb=" CA PRO C 382 " pdb=" CB PRO C 382 " ideal model delta sigma weight residual 1.532 1.525 0.006 7.10e-03 1.98e+04 7.62e-01 ... (remaining 20105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 26781 1.05 - 2.09: 437 2.09 - 3.14: 127 3.14 - 4.19: 34 4.19 - 5.24: 11 Bond angle restraints: 27390 Sorted by residual: angle pdb=" N VAL D 289 " pdb=" CA VAL D 289 " pdb=" C VAL D 289 " ideal model delta sigma weight residual 110.74 108.09 2.65 9.10e-01 1.21e+00 8.48e+00 angle pdb=" N CYS B 444 " pdb=" CA CYS B 444 " pdb=" C CYS B 444 " ideal model delta sigma weight residual 114.04 111.20 2.84 1.24e+00 6.50e-01 5.24e+00 angle pdb=" CA GLY A 572 " pdb=" C GLY A 572 " pdb=" N ASP A 573 " ideal model delta sigma weight residual 114.65 116.54 -1.89 9.20e-01 1.18e+00 4.22e+00 angle pdb=" C ILE C 269 " pdb=" N ASP C 270 " pdb=" CA ASP C 270 " ideal model delta sigma weight residual 121.80 126.70 -4.90 2.44e+00 1.68e-01 4.03e+00 angle pdb=" C ILE A 269 " pdb=" N ASP A 270 " pdb=" CA ASP A 270 " ideal model delta sigma weight residual 121.80 126.67 -4.87 2.44e+00 1.68e-01 3.99e+00 ... (remaining 27385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11308 17.87 - 35.73: 432 35.73 - 53.60: 61 53.60 - 71.46: 12 71.46 - 89.33: 3 Dihedral angle restraints: 11816 sinusoidal: 4084 harmonic: 7732 Sorted by residual: dihedral pdb=" CA TYR B 143 " pdb=" C TYR B 143 " pdb=" N ARG B 144 " pdb=" CA ARG B 144 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N LEU B 256 " pdb=" CA LEU B 256 " pdb=" CB LEU B 256 " pdb=" CG LEU B 256 " ideal model delta sinusoidal sigma weight residual -180.00 -120.43 -59.57 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU D 256 " pdb=" CA LEU D 256 " pdb=" CB LEU D 256 " pdb=" CG LEU D 256 " ideal model delta sinusoidal sigma weight residual -180.00 -120.49 -59.51 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 11813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1810 0.026 - 0.052: 918 0.052 - 0.078: 322 0.078 - 0.104: 138 0.104 - 0.130: 30 Chirality restraints: 3218 Sorted by residual: chirality pdb=" CA ILE D 381 " pdb=" N ILE D 381 " pdb=" C ILE D 381 " pdb=" CB ILE D 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 381 " pdb=" N ILE B 381 " pdb=" C ILE B 381 " pdb=" CB ILE B 381 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 3215 not shown) Planarity restraints: 3454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 680 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 681 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 680 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO C 681 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 466 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.58e+00 pdb=" N PRO D 467 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 467 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 467 " -0.018 5.00e-02 4.00e+02 ... (remaining 3451 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1021 2.74 - 3.28: 20725 3.28 - 3.82: 31069 3.82 - 4.36: 35462 4.36 - 4.90: 61054 Nonbonded interactions: 149331 Sorted by model distance: nonbonded pdb=" OD1 ASP D 270 " pdb=" OG1 THR D 273 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP B 270 " pdb=" OG1 THR B 273 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP C 270 " pdb=" OG1 THR C 273 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP A 270 " pdb=" OG1 THR A 273 " model vdw 2.201 3.040 nonbonded pdb=" O ARG C 138 " pdb=" NH1 ARG C 155 " model vdw 2.266 3.120 ... (remaining 149326 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 through 117 or (resid 118 t \ hrough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 249 or resid 251 through 333 or (resid 334 through 335 \ and (name N or name CA or name C or name O or name CB )) or resid 336 through 34 \ 4 or (resid 345 and (name N or name CA or name C or name O or name CB )) or resi \ d 346 through 368 or (resid 369 through 381 and (name N or name CA or name C or \ name O or name CB )) or resid 382 through 421 or (resid 422 and (name N or name \ CA or name C or name O or name CB )) or resid 423 through 472 or (resid 473 and \ (name N or name CA or name C or name O or name CB )) or resid 474 through 491 or \ (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 3 through 498 or (resid 499 through 500 and (name N or name CA or name C or name \ O or name CB )) or resid 501 through 561 or (resid 562 and (name N or name CA o \ r name C or name O or name CB )) or resid 563 through 572 or (resid 573 and (nam \ e N or name CA or name C or name O or name CB )) or resid 574 through 575 or (re \ sid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 th \ rough 602 or (resid 603 and (name N or name CA or name C or name O or name CB )) \ or resid 604 through 605 or (resid 606 and (name N or name CA or name C or name \ O or name CB )) or resid 607 through 638 or (resid 639 and (name N or name CA o \ r name C or name O or name CB )) or resid 640 through 654 or (resid 655 and (nam \ e N or name CA or name C or name O or name CB )) or resid 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 661 or \ (resid 662 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 3 through 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) or resid 671 or (resid 672 and (name N or name CA or name C or name O or na \ me CB )) or resid 673 through 681 or (resid 682 and (name N or name CA or name C \ or name O or name CB )) or resid 683 through 686 or (resid 687 through 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 690 \ through 692 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 3 through 694 or (resid 695 and (name N or name CA or name C or name O or name C \ B )) or resid 696 through 697 or (resid 698 through 710 and (name N or name CA o \ r name C or name O or name CB )) or resid 711 through 740)) selection = (chain 'B' and ((resid 75 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 118 or (resid 119 through 120 and (name N or n \ ame CA or name C or name O or name CB )) or resid 121 through 134 or (resid 135 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 210 or (resid 211 and (name N or name CA or name C or name O or name C \ B )) or resid 212 through 215 or (resid 216 and (name N or name CA or name C or \ name O or name CB )) or resid 217 through 249 or resid 251 through 350 or (resid \ 351 and (name N or name CA or name C or name O or name CB )) or resid 352 throu \ gh 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or \ resid 382 or (resid 383 through 385 and (name N or name CA or name C or name O \ or name CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 399 or (resid 400 and (name N \ or name CA or name C or name O or name CB )) or resid 401 through 404 or (resid \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 or (r \ esid 407 and (name N or name CA or name C or name O or name CB )) or resid 408 t \ hrough 409 or (resid 410 and (name N or name CA or name C or name O or name CB ) \ ) or resid 411 through 431 or (resid 432 and (name N or name CA or name C or nam \ e O or name CB )) or resid 433 through 434 or (resid 435 and (name N or name CA \ or name C or name O or name CB )) or resid 436 through 451 or resid 460 through \ 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) or re \ sid 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) o \ r resid 469 through 474 or (resid 475 and (name N or name CA or name C or name O \ or name CB )) or resid 476 through 478 or (resid 479 and (name N or name CA or \ name C or name O or name CB )) or resid 480 through 499 or (resid 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 502 or (resi \ d 503 and (name N or name CA or name C or name O or name CB )) or resid 504 thro \ ugh 510 or (resid 511 through 512 and (name N or name CA or name C or name O or \ name CB )) or resid 513 or (resid 514 through 518 and (name N or name CA or name \ C or name O or name CB )) or resid 519 through 520 or (resid 521 through 522 an \ d (name N or name CA or name C or name O or name CB )) or resid 523 or (resid 52 \ 9 through 535 and (name N or name CA or name C or name O or name CB )) or resid \ 536 through 612 or (resid 613 and (name N or name CA or name C or name O or name \ CB )) or resid 614 through 625 or (resid 626 and (name N or name CA or name C o \ r name O or name CB )) or resid 627 through 674 or (resid 675 and (name N or nam \ e CA or name C or name O or name CB )) or resid 676 or (resid 677 and (name N or \ name CA or name C or name O or name CB )) or resid 678 through 683 or (resid 68 \ 4 through 688 and (name N or name CA or name C or name O or name CB )) or resid \ 689 through 708 or (resid 709 through 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 739 or (resid 740 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'C' and (resid 75 through 111 or (resid 112 through 113 and (name N or na \ me CA or name C or name O or name CB )) or resid 114 through 117 or (resid 118 t \ hrough 120 and (name N or name CA or name C or name O or name CB )) or resid 121 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 249 or resid 251 through 333 or (resid 334 through 335 \ and (name N or name CA or name C or name O or name CB )) or resid 336 through 34 \ 4 or (resid 345 and (name N or name CA or name C or name O or name CB )) or resi \ d 346 through 368 or (resid 369 through 381 and (name N or name CA or name C or \ name O or name CB )) or resid 382 through 421 or (resid 422 and (name N or name \ CA or name C or name O or name CB )) or resid 423 through 472 or (resid 473 and \ (name N or name CA or name C or name O or name CB )) or resid 474 through 491 or \ (resid 492 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 3 through 498 or (resid 499 through 500 and (name N or name CA or name C or name \ O or name CB )) or resid 501 through 561 or (resid 562 and (name N or name CA o \ r name C or name O or name CB )) or resid 563 through 572 or (resid 573 and (nam \ e N or name CA or name C or name O or name CB )) or resid 574 through 575 or (re \ sid 576 and (name N or name CA or name C or name O or name CB )) or resid 577 th \ rough 602 or (resid 603 and (name N or name CA or name C or name O or name CB )) \ or resid 604 through 605 or (resid 606 and (name N or name CA or name C or name \ O or name CB )) or resid 607 through 638 or (resid 639 and (name N or name CA o \ r name C or name O or name CB )) or resid 640 through 654 or (resid 655 and (nam \ e N or name CA or name C or name O or name CB )) or resid 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 661 or \ (resid 662 and (name N or name CA or name C or name O or name CB )) or resid 66 \ 3 through 669 or (resid 670 and (name N or name CA or name C or name O or name C \ B )) or resid 671 or (resid 672 and (name N or name CA or name C or name O or na \ me CB )) or resid 673 through 681 or (resid 682 and (name N or name CA or name C \ or name O or name CB )) or resid 683 through 686 or (resid 687 through 688 and \ (name N or name CA or name C or name O or name CB )) or resid 689 or (resid 690 \ through 692 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 3 through 694 or (resid 695 and (name N or name CA or name C or name O or name C \ B )) or resid 696 through 697 or (resid 698 through 710 and (name N or name CA o \ r name C or name O or name CB )) or resid 711 through 740)) selection = (chain 'D' and ((resid 75 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 through 118 or (resid 119 through 120 and (name N or n \ ame CA or name C or name O or name CB )) or resid 121 through 134 or (resid 135 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 210 or (resid 211 and (name N or name CA or name C or name O or name C \ B )) or resid 212 through 215 or (resid 216 and (name N or name CA or name C or \ name O or name CB )) or resid 217 through 249 or resid 251 through 350 or (resid \ 351 and (name N or name CA or name C or name O or name CB )) or resid 352 throu \ gh 380 or (resid 381 and (name N or name CA or name C or name O or name CB )) or \ resid 382 or (resid 383 through 385 and (name N or name CA or name C or name O \ or name CB )) or resid 386 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 399 or (resid 400 and (name N \ or name CA or name C or name O or name CB )) or resid 401 through 404 or (resid \ 405 and (name N or name CA or name C or name O or name CB )) or resid 406 or (r \ esid 407 and (name N or name CA or name C or name O or name CB )) or resid 408 t \ hrough 409 or (resid 410 and (name N or name CA or name C or name O or name CB ) \ ) or resid 411 through 431 or (resid 432 and (name N or name CA or name C or nam \ e O or name CB )) or resid 433 through 434 or (resid 435 and (name N or name CA \ or name C or name O or name CB )) or resid 436 through 451 or resid 460 through \ 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) or re \ sid 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) o \ r resid 469 through 474 or (resid 475 and (name N or name CA or name C or name O \ or name CB )) or resid 476 through 478 or (resid 479 and (name N or name CA or \ name C or name O or name CB )) or resid 480 through 499 or (resid 500 and (name \ N or name CA or name C or name O or name CB )) or resid 501 through 502 or (resi \ d 503 and (name N or name CA or name C or name O or name CB )) or resid 504 thro \ ugh 510 or (resid 511 through 512 and (name N or name CA or name C or name O or \ name CB )) or resid 513 or (resid 514 through 518 and (name N or name CA or name \ C or name O or name CB )) or resid 519 through 520 or (resid 521 through 522 an \ d (name N or name CA or name C or name O or name CB )) or resid 523 or (resid 52 \ 9 through 535 and (name N or name CA or name C or name O or name CB )) or resid \ 536 through 612 or (resid 613 and (name N or name CA or name C or name O or name \ CB )) or resid 614 through 625 or (resid 626 and (name N or name CA or name C o \ r name O or name CB )) or resid 627 through 674 or (resid 675 and (name N or nam \ e CA or name C or name O or name CB )) or resid 676 or (resid 677 and (name N or \ name CA or name C or name O or name CB )) or resid 678 through 683 or (resid 68 \ 4 through 688 and (name N or name CA or name C or name O or name CB )) or resid \ 689 through 708 or (resid 709 through 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 739 or (resid 740 and (name N or name CA \ or name C or name O or name CB )))) } 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=0.50 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.850 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 0.038 20110 Z= 0.088 Angle : 0.403 5.236 27390 Z= 0.217 Chirality : 0.037 0.130 3218 Planarity : 0.003 0.040 3454 Dihedral : 9.751 89.326 6844 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 1.03 % Allowed : 7.52 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2616 helix: 0.51 (0.13), residues: 1562 sheet: 1.52 (0.52), residues: 86 loop : -0.28 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.011 0.001 TYR D 143 PHE 0.011 0.001 PHE C 266 TRP 0.007 0.001 TRP D 272 HIS 0.002 0.001 HIS A 683 Details of bonding type rmsd covalent geometry : bond 0.00181 (20110) covalent geometry : angle 0.40278 (27390) hydrogen bonds : bond 0.29830 ( 1138) hydrogen bonds : angle 6.77727 ( 3231) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.8256 (t80) cc_final: 0.7706 (t80) REVERT: A 169 MET cc_start: 0.8244 (mtp) cc_final: 0.7929 (mtm) REVERT: A 378 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6324 (mm) REVERT: A 422 GLU cc_start: 0.8332 (pt0) cc_final: 0.7914 (pp20) REVERT: A 484 TYR cc_start: 0.8730 (m-80) cc_final: 0.8342 (m-80) REVERT: A 560 ASP cc_start: 0.7447 (t0) cc_final: 0.7137 (t0) REVERT: A 563 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 599 TYR cc_start: 0.7162 (t80) cc_final: 0.6846 (t80) REVERT: A 655 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8323 (mmmm) REVERT: A 672 ASN cc_start: 0.7760 (m110) cc_final: 0.7355 (p0) REVERT: A 696 GLN cc_start: 0.8762 (mt0) cc_final: 0.8421 (mt0) REVERT: B 227 TYR cc_start: 0.9162 (t80) cc_final: 0.8908 (t80) REVERT: B 365 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8275 (tpt90) REVERT: B 405 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6719 (mtm-85) REVERT: B 432 GLU cc_start: 0.8409 (pt0) cc_final: 0.7949 (pm20) REVERT: B 558 TYR cc_start: 0.8474 (m-80) cc_final: 0.7948 (m-80) REVERT: B 565 LYS cc_start: 0.8654 (mttp) cc_final: 0.8051 (ptpp) REVERT: B 569 ARG cc_start: 0.8391 (ptp90) cc_final: 0.8133 (ptt-90) REVERT: C 156 TYR cc_start: 0.8231 (t80) cc_final: 0.7680 (t80) REVERT: C 169 MET cc_start: 0.8211 (mtp) cc_final: 0.7883 (mtm) REVERT: C 378 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6497 (mm) REVERT: C 484 TYR cc_start: 0.8624 (m-80) cc_final: 0.8239 (m-80) REVERT: C 548 LEU cc_start: 0.8645 (mt) cc_final: 0.8355 (mt) REVERT: C 560 ASP cc_start: 0.7453 (t0) cc_final: 0.7106 (t0) REVERT: C 563 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8383 (tp-100) REVERT: C 655 LYS cc_start: 0.8668 (ttmt) cc_final: 0.8326 (mmmm) REVERT: C 667 ASN cc_start: 0.8869 (m-40) cc_final: 0.8593 (m110) REVERT: C 672 ASN cc_start: 0.8122 (m-40) cc_final: 0.7837 (p0) REVERT: D 147 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7253 (t80) REVERT: D 164 ASP cc_start: 0.8032 (t0) cc_final: 0.7820 (t0) REVERT: D 365 ARG cc_start: 0.8809 (mmm-85) cc_final: 0.8312 (tpt90) REVERT: D 405 ARG cc_start: 0.6800 (mtm-85) cc_final: 0.6555 (mtm-85) REVERT: D 432 GLU cc_start: 0.8420 (pt0) cc_final: 0.7962 (pm20) REVERT: D 558 TYR cc_start: 0.8472 (m-80) cc_final: 0.8190 (m-80) REVERT: D 561 LEU cc_start: 0.8745 (tp) cc_final: 0.8245 (tp) REVERT: D 565 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8164 (mtmt) outliers start: 19 outliers final: 6 residues processed: 301 average time/residue: 0.1789 time to fit residues: 79.3611 Evaluate side-chains 224 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 215 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 505 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 575 ASN A 683 HIS B 247 GLN B 439 GLN B 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 575 ASN C 644 ASN C 667 ASN C 683 HIS D 247 GLN D 348 ASN D 445 HIS D 469 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.169047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.111621 restraints weight = 64106.632| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 4.87 r_work: 0.3169 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20110 Z= 0.138 Angle : 0.558 7.091 27390 Z= 0.295 Chirality : 0.041 0.224 3218 Planarity : 0.004 0.041 3454 Dihedral : 4.209 58.991 2897 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 1.31 % Allowed : 11.11 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2616 helix: 1.14 (0.13), residues: 1600 sheet: 1.35 (0.48), residues: 102 loop : -0.37 (0.22), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 487 TYR 0.022 0.001 TYR D 593 PHE 0.017 0.002 PHE C 539 TRP 0.006 0.001 TRP B 272 HIS 0.006 0.001 HIS C 363 Details of bonding type rmsd covalent geometry : bond 0.00280 (20110) covalent geometry : angle 0.55784 (27390) hydrogen bonds : bond 0.06284 ( 1138) hydrogen bonds : angle 4.45274 ( 3231) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.772 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 156 TYR cc_start: 0.7875 (t80) cc_final: 0.7302 (t80) REVERT: A 169 MET cc_start: 0.8538 (mtp) cc_final: 0.8313 (mtm) REVERT: A 378 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6511 (mm) REVERT: A 422 GLU cc_start: 0.8321 (pt0) cc_final: 0.7919 (pp20) REVERT: A 539 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7661 (t80) REVERT: A 560 ASP cc_start: 0.7386 (t0) cc_final: 0.7107 (t0) REVERT: A 672 ASN cc_start: 0.7823 (m110) cc_final: 0.7511 (p0) REVERT: A 678 HIS cc_start: 0.7354 (t-90) cc_final: 0.7152 (t70) REVERT: A 696 GLN cc_start: 0.8773 (mt0) cc_final: 0.8353 (mt0) REVERT: B 344 MET cc_start: 0.8905 (tpp) cc_final: 0.8699 (tpp) REVERT: B 365 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8492 (tpt90) REVERT: B 405 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.7022 (mtm-85) REVERT: B 432 GLU cc_start: 0.8738 (pt0) cc_final: 0.8407 (pm20) REVERT: B 558 TYR cc_start: 0.8279 (m-80) cc_final: 0.7885 (m-80) REVERT: B 569 ARG cc_start: 0.8754 (ptp90) cc_final: 0.8496 (ptt-90) REVERT: C 156 TYR cc_start: 0.7881 (t80) cc_final: 0.7336 (t80) REVERT: C 169 MET cc_start: 0.8569 (mtp) cc_final: 0.8337 (mtm) REVERT: C 205 MET cc_start: 0.8669 (ttp) cc_final: 0.8372 (ttm) REVERT: C 378 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6609 (mm) REVERT: C 560 ASP cc_start: 0.7629 (t0) cc_final: 0.7323 (t0) REVERT: C 563 GLN cc_start: 0.8994 (tp40) cc_final: 0.8550 (tp-100) REVERT: C 672 ASN cc_start: 0.8301 (m-40) cc_final: 0.8055 (p0) REVERT: D 147 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.7294 (t80) REVERT: D 365 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8585 (tpt90) REVERT: D 405 ARG cc_start: 0.7065 (mtm-85) cc_final: 0.6818 (mtm-85) REVERT: D 432 GLU cc_start: 0.8714 (pt0) cc_final: 0.8386 (pm20) REVERT: D 558 TYR cc_start: 0.8139 (m-80) cc_final: 0.7867 (m-80) outliers start: 22 outliers final: 9 residues processed: 260 average time/residue: 0.1620 time to fit residues: 63.6851 Evaluate side-chains 219 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 505 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 116 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 61 optimal weight: 50.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** 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 = 0.4291 r_free = 0.4291 target = 0.167679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.098778 restraints weight = 52238.186| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.81 r_work: 0.3224 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20110 Z= 0.150 Angle : 0.544 7.592 27390 Z= 0.284 Chirality : 0.041 0.175 3218 Planarity : 0.004 0.040 3454 Dihedral : 4.130 59.471 2893 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 1.69 % Allowed : 12.53 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2616 helix: 1.48 (0.13), residues: 1606 sheet: 1.32 (0.48), residues: 102 loop : -0.42 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 487 TYR 0.018 0.001 TYR D 280 PHE 0.026 0.002 PHE B 336 TRP 0.006 0.001 TRP D 272 HIS 0.012 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00342 (20110) covalent geometry : angle 0.54362 (27390) hydrogen bonds : bond 0.05501 ( 1138) hydrogen bonds : angle 4.03427 ( 3231) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.829 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 156 TYR cc_start: 0.7804 (t80) cc_final: 0.7289 (t80) REVERT: A 422 GLU cc_start: 0.8272 (pt0) cc_final: 0.7756 (pp20) REVERT: A 539 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7734 (t80) REVERT: A 650 CYS cc_start: 0.8322 (p) cc_final: 0.7723 (p) REVERT: A 672 ASN cc_start: 0.7841 (m110) cc_final: 0.7523 (p0) REVERT: A 678 HIS cc_start: 0.7442 (t-90) cc_final: 0.7204 (t70) REVERT: A 696 GLN cc_start: 0.8864 (mt0) cc_final: 0.8401 (mt0) REVERT: B 365 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8501 (tpt90) REVERT: B 405 ARG cc_start: 0.7339 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: B 432 GLU cc_start: 0.8743 (pt0) cc_final: 0.8408 (pm20) REVERT: B 438 ASP cc_start: 0.8499 (p0) cc_final: 0.8240 (p0) REVERT: B 558 TYR cc_start: 0.8134 (m-80) cc_final: 0.7844 (m-80) REVERT: C 156 TYR cc_start: 0.7799 (t80) cc_final: 0.7286 (t80) REVERT: C 378 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6570 (mm) REVERT: C 560 ASP cc_start: 0.7672 (t0) cc_final: 0.7344 (t0) REVERT: C 563 GLN cc_start: 0.8965 (tp40) cc_final: 0.8541 (tp-100) REVERT: C 672 ASN cc_start: 0.8232 (m-40) cc_final: 0.7990 (p0) REVERT: D 147 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7617 (t80) REVERT: D 365 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8556 (tpt90) REVERT: D 405 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6887 (mtm-85) REVERT: D 432 GLU cc_start: 0.8788 (pt0) cc_final: 0.8462 (pm20) outliers start: 29 outliers final: 12 residues processed: 239 average time/residue: 0.1579 time to fit residues: 57.6259 Evaluate side-chains 214 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 336 PHE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS A 644 ASN A 667 ASN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 HIS C 445 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.168045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110153 restraints weight = 62963.249| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.93 r_work: 0.3163 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20110 Z= 0.132 Angle : 0.532 9.006 27390 Z= 0.274 Chirality : 0.041 0.179 3218 Planarity : 0.004 0.040 3454 Dihedral : 3.966 59.201 2889 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.74 % Allowed : 13.13 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.17), residues: 2616 helix: 1.63 (0.13), residues: 1608 sheet: 1.42 (0.49), residues: 102 loop : -0.54 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.019 0.001 TYR A 599 PHE 0.027 0.001 PHE B 336 TRP 0.007 0.001 TRP D 272 HIS 0.013 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00301 (20110) covalent geometry : angle 0.53230 (27390) hydrogen bonds : bond 0.04808 ( 1138) hydrogen bonds : angle 3.85861 ( 3231) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.7759 (t80) cc_final: 0.7263 (t80) REVERT: A 323 MET cc_start: 0.9021 (tpp) cc_final: 0.8792 (mmm) REVERT: A 378 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6087 (mm) REVERT: A 422 GLU cc_start: 0.8169 (pt0) cc_final: 0.7791 (pp20) REVERT: A 650 CYS cc_start: 0.8364 (p) cc_final: 0.7733 (p) REVERT: A 672 ASN cc_start: 0.7721 (m110) cc_final: 0.7367 (p0) REVERT: A 678 HIS cc_start: 0.7436 (t-90) cc_final: 0.7169 (t-90) REVERT: A 696 GLN cc_start: 0.8875 (mt0) cc_final: 0.8391 (mt0) REVERT: B 344 MET cc_start: 0.8997 (tpp) cc_final: 0.8542 (mmm) REVERT: B 365 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8603 (tpt90) REVERT: B 405 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.7071 (mtm-85) REVERT: B 432 GLU cc_start: 0.8675 (pt0) cc_final: 0.8347 (pm20) REVERT: B 438 ASP cc_start: 0.8489 (p0) cc_final: 0.8236 (p0) REVERT: B 558 TYR cc_start: 0.8127 (m-80) cc_final: 0.7865 (m-80) REVERT: B 563 GLN cc_start: 0.9311 (tt0) cc_final: 0.9072 (mm110) REVERT: C 156 TYR cc_start: 0.7766 (t80) cc_final: 0.7265 (t80) REVERT: C 378 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6599 (mm) REVERT: C 563 GLN cc_start: 0.8937 (tp40) cc_final: 0.8482 (tp-100) REVERT: C 593 TYR cc_start: 0.7833 (m-10) cc_final: 0.7215 (m-10) REVERT: C 672 ASN cc_start: 0.8125 (m-40) cc_final: 0.7859 (p0) REVERT: D 147 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7471 (t80) REVERT: D 365 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8561 (tpt90) REVERT: D 405 ARG cc_start: 0.7132 (mtm-85) cc_final: 0.6872 (mtm-85) REVERT: D 432 GLU cc_start: 0.8689 (pt0) cc_final: 0.8360 (pm20) outliers start: 30 outliers final: 17 residues processed: 237 average time/residue: 0.1517 time to fit residues: 55.4112 Evaluate side-chains 223 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 114 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 232 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 219 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 GLN A 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN D 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.169521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110674 restraints weight = 59890.257| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 4.50 r_work: 0.3220 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20110 Z= 0.110 Angle : 0.523 10.728 27390 Z= 0.264 Chirality : 0.040 0.156 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.902 59.948 2889 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 1.53 % Allowed : 13.94 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.17), residues: 2616 helix: 1.79 (0.13), residues: 1606 sheet: 1.70 (0.49), residues: 98 loop : -0.55 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.016 0.001 TYR D 593 PHE 0.017 0.001 PHE D 336 TRP 0.007 0.001 TRP D 272 HIS 0.014 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00235 (20110) covalent geometry : angle 0.52320 (27390) hydrogen bonds : bond 0.04271 ( 1138) hydrogen bonds : angle 3.69124 ( 3231) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.801 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 156 TYR cc_start: 0.7702 (t80) cc_final: 0.7221 (t80) REVERT: A 323 MET cc_start: 0.8963 (tpp) cc_final: 0.8754 (mmm) REVERT: A 378 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6127 (mm) REVERT: A 422 GLU cc_start: 0.8096 (pt0) cc_final: 0.7800 (pp20) REVERT: A 650 CYS cc_start: 0.8355 (p) cc_final: 0.7753 (p) REVERT: A 672 ASN cc_start: 0.7652 (m110) cc_final: 0.7281 (p0) REVERT: A 678 HIS cc_start: 0.7519 (t-90) cc_final: 0.7256 (t-90) REVERT: A 696 GLN cc_start: 0.8904 (mt0) cc_final: 0.8438 (mt0) REVERT: B 344 MET cc_start: 0.9018 (tpp) cc_final: 0.8495 (tpt) REVERT: B 365 ARG cc_start: 0.8986 (mmm160) cc_final: 0.8540 (tpt90) REVERT: B 405 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.7003 (mtm-85) REVERT: B 432 GLU cc_start: 0.8656 (pt0) cc_final: 0.8334 (pm20) REVERT: B 438 ASP cc_start: 0.8486 (p0) cc_final: 0.8221 (p0) REVERT: B 558 TYR cc_start: 0.8117 (m-80) cc_final: 0.7901 (m-80) REVERT: B 649 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7522 (tt) REVERT: C 156 TYR cc_start: 0.7698 (t80) cc_final: 0.7203 (t80) REVERT: C 323 MET cc_start: 0.9008 (tpp) cc_final: 0.8805 (mmm) REVERT: C 378 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6608 (mm) REVERT: C 563 GLN cc_start: 0.8950 (tp40) cc_final: 0.8483 (tp-100) REVERT: C 672 ASN cc_start: 0.8145 (m-40) cc_final: 0.7824 (p0) REVERT: D 147 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7370 (t80) REVERT: D 344 MET cc_start: 0.8853 (mmm) cc_final: 0.8503 (mmm) REVERT: D 365 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8595 (tpt170) REVERT: D 405 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6840 (mtm-85) REVERT: D 432 GLU cc_start: 0.8634 (pt0) cc_final: 0.8316 (pm20) REVERT: D 558 TYR cc_start: 0.7768 (m-80) cc_final: 0.7506 (m-80) outliers start: 26 outliers final: 16 residues processed: 240 average time/residue: 0.1611 time to fit residues: 58.9812 Evaluate side-chains 224 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 242 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 145 optimal weight: 0.0980 chunk 142 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 172 optimal weight: 7.9990 chunk 175 optimal weight: 30.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS A 367 GLN A 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.170040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102793 restraints weight = 49865.114| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.78 r_work: 0.3284 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20110 Z= 0.104 Angle : 0.515 9.497 27390 Z= 0.259 Chirality : 0.040 0.148 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.841 59.777 2889 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 1.69 % Allowed : 13.94 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.17), residues: 2616 helix: 1.94 (0.13), residues: 1602 sheet: 1.86 (0.48), residues: 94 loop : -0.54 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.014 0.001 TYR C 280 PHE 0.032 0.001 PHE B 336 TRP 0.007 0.001 TRP B 272 HIS 0.014 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00219 (20110) covalent geometry : angle 0.51465 (27390) hydrogen bonds : bond 0.03967 ( 1138) hydrogen bonds : angle 3.59321 ( 3231) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.7678 (t80) cc_final: 0.7221 (t80) REVERT: A 323 MET cc_start: 0.8944 (tpp) cc_final: 0.8736 (mmm) REVERT: A 422 GLU cc_start: 0.8157 (pt0) cc_final: 0.7843 (pp20) REVERT: A 539 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7685 (t80) REVERT: A 672 ASN cc_start: 0.7749 (m110) cc_final: 0.7344 (p0) REVERT: A 678 HIS cc_start: 0.7498 (t-90) cc_final: 0.7248 (t70) REVERT: A 696 GLN cc_start: 0.8885 (mt0) cc_final: 0.8490 (mt0) REVERT: B 344 MET cc_start: 0.9027 (tpp) cc_final: 0.8516 (tpt) REVERT: B 365 ARG cc_start: 0.8981 (mmm160) cc_final: 0.8521 (tpt90) REVERT: B 405 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7031 (mtm-85) REVERT: B 432 GLU cc_start: 0.8779 (pt0) cc_final: 0.8450 (pm20) REVERT: B 438 ASP cc_start: 0.8524 (p0) cc_final: 0.8228 (p0) REVERT: B 476 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8137 (mt) REVERT: B 649 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7474 (tt) REVERT: C 156 TYR cc_start: 0.7665 (t80) cc_final: 0.7184 (t80) REVERT: C 378 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6577 (mm) REVERT: C 563 GLN cc_start: 0.8976 (tp40) cc_final: 0.8483 (tp-100) REVERT: D 147 TYR cc_start: 0.7750 (OUTLIER) cc_final: 0.7247 (t80) REVERT: D 344 MET cc_start: 0.8837 (mmm) cc_final: 0.8591 (mmm) REVERT: D 365 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8543 (tpt90) REVERT: D 405 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6888 (mtm-85) REVERT: D 432 GLU cc_start: 0.8784 (pt0) cc_final: 0.8460 (pm20) REVERT: D 558 TYR cc_start: 0.7741 (m-80) cc_final: 0.7466 (m-80) outliers start: 29 outliers final: 18 residues processed: 234 average time/residue: 0.1547 time to fit residues: 55.6201 Evaluate side-chains 229 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 94 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 40 optimal weight: 0.0470 chunk 227 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN A 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.169183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108551 restraints weight = 54583.349| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.19 r_work: 0.3201 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20110 Z= 0.115 Angle : 0.521 9.999 27390 Z= 0.262 Chirality : 0.040 0.144 3218 Planarity : 0.003 0.042 3454 Dihedral : 3.847 59.823 2889 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 1.74 % Allowed : 14.32 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.17), residues: 2616 helix: 1.96 (0.13), residues: 1608 sheet: 1.86 (0.48), residues: 94 loop : -0.52 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.020 0.001 TYR D 593 PHE 0.017 0.001 PHE D 336 TRP 0.006 0.001 TRP B 272 HIS 0.014 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00258 (20110) covalent geometry : angle 0.52099 (27390) hydrogen bonds : bond 0.04135 ( 1138) hydrogen bonds : angle 3.58027 ( 3231) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.718 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 156 TYR cc_start: 0.7629 (t80) cc_final: 0.7162 (t80) REVERT: A 323 MET cc_start: 0.8996 (tpp) cc_final: 0.8772 (mmm) REVERT: A 378 LEU cc_start: 0.6456 (mm) cc_final: 0.6071 (mm) REVERT: A 422 GLU cc_start: 0.8035 (pt0) cc_final: 0.7738 (pp20) REVERT: A 539 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 672 ASN cc_start: 0.7826 (m110) cc_final: 0.7405 (p0) REVERT: A 678 HIS cc_start: 0.7516 (t-90) cc_final: 0.7240 (t70) REVERT: A 696 GLN cc_start: 0.8921 (mt0) cc_final: 0.8553 (mt0) REVERT: B 344 MET cc_start: 0.9000 (tpp) cc_final: 0.8514 (tpt) REVERT: B 365 ARG cc_start: 0.8967 (mmm160) cc_final: 0.8576 (tpt90) REVERT: B 405 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7058 (mtm-85) REVERT: B 432 GLU cc_start: 0.8630 (pt0) cc_final: 0.8301 (pm20) REVERT: B 438 ASP cc_start: 0.8473 (p0) cc_final: 0.8172 (p0) REVERT: B 476 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8132 (mt) REVERT: B 649 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7487 (tt) REVERT: C 156 TYR cc_start: 0.7638 (t80) cc_final: 0.7159 (t80) REVERT: C 347 MET cc_start: 0.8461 (ttp) cc_final: 0.8253 (ttp) REVERT: C 378 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6535 (mm) REVERT: C 563 GLN cc_start: 0.8977 (tp40) cc_final: 0.8495 (tp-100) REVERT: D 147 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.7281 (t80) REVERT: D 344 MET cc_start: 0.8791 (mmm) cc_final: 0.8556 (mmm) REVERT: D 365 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8564 (tpt170) REVERT: D 405 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6850 (mtm-85) REVERT: D 432 GLU cc_start: 0.8608 (pt0) cc_final: 0.8291 (pm20) REVERT: D 558 TYR cc_start: 0.7748 (m-80) cc_final: 0.7468 (m-80) outliers start: 30 outliers final: 21 residues processed: 235 average time/residue: 0.1520 time to fit residues: 55.2999 Evaluate side-chains 233 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 181 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 HIS B 348 ASN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.165903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096886 restraints weight = 51763.204| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.76 r_work: 0.3169 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20110 Z= 0.193 Angle : 0.585 9.050 27390 Z= 0.297 Chirality : 0.043 0.167 3218 Planarity : 0.004 0.040 3454 Dihedral : 4.043 59.884 2889 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 1.74 % Allowed : 14.49 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.17), residues: 2616 helix: 1.81 (0.13), residues: 1610 sheet: 1.67 (0.50), residues: 96 loop : -0.46 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 487 TYR 0.020 0.002 TYR B 280 PHE 0.020 0.002 PHE B 336 TRP 0.008 0.001 TRP D 85 HIS 0.015 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00468 (20110) covalent geometry : angle 0.58453 (27390) hydrogen bonds : bond 0.05139 ( 1138) hydrogen bonds : angle 3.75758 ( 3231) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 TYR cc_start: 0.7790 (t80) cc_final: 0.7300 (t80) REVERT: A 378 LEU cc_start: 0.6508 (mm) cc_final: 0.6157 (mm) REVERT: A 422 GLU cc_start: 0.8195 (pt0) cc_final: 0.7773 (pp20) REVERT: A 672 ASN cc_start: 0.7868 (m110) cc_final: 0.7407 (p0) REVERT: A 678 HIS cc_start: 0.7507 (t-90) cc_final: 0.7242 (t70) REVERT: A 696 GLN cc_start: 0.8888 (mt0) cc_final: 0.8617 (mt0) REVERT: B 344 MET cc_start: 0.9014 (tpp) cc_final: 0.8767 (tpp) REVERT: B 365 ARG cc_start: 0.9040 (mmm160) cc_final: 0.8671 (tpt90) REVERT: B 405 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.7151 (mtm-85) REVERT: B 428 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8207 (mm-30) REVERT: B 432 GLU cc_start: 0.8757 (pt0) cc_final: 0.8433 (pm20) REVERT: B 438 ASP cc_start: 0.8526 (p0) cc_final: 0.8217 (p0) REVERT: B 569 ARG cc_start: 0.8770 (ptp90) cc_final: 0.8494 (ptt-90) REVERT: C 82 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7907 (m-10) REVERT: C 563 GLN cc_start: 0.9000 (tp40) cc_final: 0.8509 (tp-100) REVERT: C 606 ASP cc_start: 0.8823 (t0) cc_final: 0.8462 (t0) REVERT: C 682 LEU cc_start: 0.8692 (mm) cc_final: 0.8454 (mp) REVERT: D 147 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7568 (t80) REVERT: D 164 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: D 344 MET cc_start: 0.8781 (mmm) cc_final: 0.8497 (mmm) REVERT: D 365 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8622 (tpt90) REVERT: D 405 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: D 432 GLU cc_start: 0.8778 (pt0) cc_final: 0.8456 (pm20) REVERT: D 558 TYR cc_start: 0.7781 (m-80) cc_final: 0.7492 (m-80) outliers start: 30 outliers final: 21 residues processed: 221 average time/residue: 0.1488 time to fit residues: 50.8155 Evaluate side-chains 221 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 205 MET Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 500 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 76 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 97 optimal weight: 0.0270 chunk 178 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS B 500 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101904 restraints weight = 50061.309| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.16 r_work: 0.3237 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20110 Z= 0.110 Angle : 0.544 9.613 27390 Z= 0.271 Chirality : 0.040 0.179 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.799 59.678 2887 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 1.47 % Allowed : 14.92 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.17), residues: 2616 helix: 1.97 (0.13), residues: 1610 sheet: 1.77 (0.48), residues: 94 loop : -0.54 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 487 TYR 0.014 0.001 TYR D 143 PHE 0.032 0.001 PHE B 336 TRP 0.007 0.001 TRP B 272 HIS 0.015 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00237 (20110) covalent geometry : angle 0.54380 (27390) hydrogen bonds : bond 0.04180 ( 1138) hydrogen bonds : angle 3.56710 ( 3231) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.773 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 156 TYR cc_start: 0.7733 (t80) cc_final: 0.7264 (t80) REVERT: A 378 LEU cc_start: 0.6395 (mm) cc_final: 0.6038 (mm) REVERT: A 422 GLU cc_start: 0.8148 (pt0) cc_final: 0.7780 (pp20) REVERT: A 672 ASN cc_start: 0.7824 (m110) cc_final: 0.7330 (p0) REVERT: A 678 HIS cc_start: 0.7548 (t-90) cc_final: 0.7327 (t70) REVERT: A 696 GLN cc_start: 0.8849 (mt0) cc_final: 0.8612 (mt0) REVERT: B 344 MET cc_start: 0.8990 (tpp) cc_final: 0.8626 (mmm) REVERT: B 365 ARG cc_start: 0.8997 (mmm160) cc_final: 0.8584 (tpt90) REVERT: B 405 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7117 (mtm-85) REVERT: B 428 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 432 GLU cc_start: 0.8763 (pt0) cc_final: 0.8427 (pm20) REVERT: B 438 ASP cc_start: 0.8487 (p0) cc_final: 0.8204 (p0) REVERT: B 649 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7522 (tt) REVERT: C 156 TYR cc_start: 0.7720 (t80) cc_final: 0.7252 (t80) REVERT: C 347 MET cc_start: 0.8404 (ttp) cc_final: 0.8101 (ptt) REVERT: C 378 LEU cc_start: 0.6533 (mm) cc_final: 0.6161 (mm) REVERT: C 424 PHE cc_start: 0.8777 (m-10) cc_final: 0.8554 (m-80) REVERT: C 563 GLN cc_start: 0.9006 (tp40) cc_final: 0.8538 (tp-100) REVERT: C 593 TYR cc_start: 0.7815 (m-10) cc_final: 0.7175 (m-10) REVERT: C 606 ASP cc_start: 0.8822 (t0) cc_final: 0.8457 (t0) REVERT: D 147 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7355 (t80) REVERT: D 164 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: D 344 MET cc_start: 0.8825 (mmm) cc_final: 0.8560 (mmm) REVERT: D 365 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8574 (tpt170) REVERT: D 405 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6948 (mtm-85) REVERT: D 432 GLU cc_start: 0.8776 (pt0) cc_final: 0.8457 (pm20) REVERT: D 558 TYR cc_start: 0.7744 (m-80) cc_final: 0.7466 (m-80) outliers start: 25 outliers final: 18 residues processed: 229 average time/residue: 0.1500 time to fit residues: 53.6226 Evaluate side-chains 230 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Chi-restraints excluded: chain D residue 500 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 130 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 185 optimal weight: 8.9990 chunk 60 optimal weight: 0.3980 chunk 219 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.169342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111040 restraints weight = 60858.768| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.50 r_work: 0.3185 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20110 Z= 0.109 Angle : 0.547 12.620 27390 Z= 0.272 Chirality : 0.040 0.178 3218 Planarity : 0.003 0.044 3454 Dihedral : 3.746 59.503 2887 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 1.36 % Allowed : 14.98 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2616 helix: 1.99 (0.13), residues: 1612 sheet: 1.68 (0.48), residues: 94 loop : -0.44 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.013 0.001 TYR C 280 PHE 0.017 0.001 PHE D 336 TRP 0.007 0.001 TRP B 272 HIS 0.015 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00238 (20110) covalent geometry : angle 0.54672 (27390) hydrogen bonds : bond 0.04021 ( 1138) hydrogen bonds : angle 3.52303 ( 3231) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.759 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 156 TYR cc_start: 0.7630 (t80) cc_final: 0.7167 (t80) REVERT: A 323 MET cc_start: 0.8980 (tpp) cc_final: 0.8763 (mmm) REVERT: A 378 LEU cc_start: 0.6418 (mm) cc_final: 0.6064 (mm) REVERT: A 422 GLU cc_start: 0.7944 (pt0) cc_final: 0.7676 (mt-10) REVERT: A 672 ASN cc_start: 0.7779 (m110) cc_final: 0.7260 (p0) REVERT: A 696 GLN cc_start: 0.8781 (mt0) cc_final: 0.8559 (mt0) REVERT: B 344 MET cc_start: 0.8895 (tpp) cc_final: 0.8528 (mmm) REVERT: B 365 ARG cc_start: 0.9001 (mmm160) cc_final: 0.8569 (tpt90) REVERT: B 405 ARG cc_start: 0.7380 (mtm-85) cc_final: 0.7054 (mtm-85) REVERT: B 428 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 432 GLU cc_start: 0.8678 (pt0) cc_final: 0.8328 (pm20) REVERT: B 438 ASP cc_start: 0.8467 (p0) cc_final: 0.8184 (p0) REVERT: B 649 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7573 (tt) REVERT: C 156 TYR cc_start: 0.7624 (t80) cc_final: 0.7164 (t80) REVERT: C 347 MET cc_start: 0.8351 (ttp) cc_final: 0.8061 (ptt) REVERT: C 378 LEU cc_start: 0.6509 (mm) cc_final: 0.6150 (mm) REVERT: C 424 PHE cc_start: 0.8752 (m-10) cc_final: 0.8523 (m-80) REVERT: C 563 GLN cc_start: 0.8996 (tp40) cc_final: 0.8505 (tp-100) REVERT: C 593 TYR cc_start: 0.7808 (m-10) cc_final: 0.7203 (m-10) REVERT: C 606 ASP cc_start: 0.8820 (t0) cc_final: 0.8449 (t0) REVERT: D 147 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7223 (t80) REVERT: D 164 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: D 344 MET cc_start: 0.8764 (mmm) cc_final: 0.8514 (mmm) REVERT: D 365 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8572 (tpt170) REVERT: D 405 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: D 432 GLU cc_start: 0.8678 (pt0) cc_final: 0.8344 (pm20) REVERT: D 558 TYR cc_start: 0.7717 (m-80) cc_final: 0.7440 (m-80) outliers start: 23 outliers final: 16 residues processed: 230 average time/residue: 0.1485 time to fit residues: 53.0927 Evaluate side-chains 230 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 336 PHE Chi-restraints excluded: chain D residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 234 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS B 469 HIS B 500 GLN ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.169145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107604 restraints weight = 56666.683| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.38 r_work: 0.3241 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20110 Z= 0.115 Angle : 0.551 11.668 27390 Z= 0.273 Chirality : 0.040 0.182 3218 Planarity : 0.003 0.043 3454 Dihedral : 3.738 59.221 2887 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 1.53 % Allowed : 15.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2616 helix: 2.01 (0.13), residues: 1614 sheet: 1.73 (0.48), residues: 94 loop : -0.41 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 487 TYR 0.014 0.001 TYR C 280 PHE 0.018 0.001 PHE B 336 TRP 0.006 0.001 TRP D 272 HIS 0.016 0.001 HIS C 678 Details of bonding type rmsd covalent geometry : bond 0.00259 (20110) covalent geometry : angle 0.55075 (27390) hydrogen bonds : bond 0.04016 ( 1138) hydrogen bonds : angle 3.50590 ( 3231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7593.43 seconds wall clock time: 130 minutes 9.51 seconds (7809.51 seconds total)