Starting phenix.real_space_refine on Tue May 20 10:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jec_36185/05_2025/8jec_36185.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jec_36185/05_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_36185/05_2025/8jec_36185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jec_36185/05_2025/8jec_36185.map" model { file = "/net/cci-nas-00/data/ceres_data/8jec_36185/05_2025/8jec_36185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jec_36185/05_2025/8jec_36185.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 11} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 241 bond proxies already assigned to first conformer: 5071 Time building chain proxies: 21.11, per 1000 atoms: 1.07 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: 5.54 Conformation dependent library (CDL) restraints added in 4.9 seconds 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: 2.12 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: 6.82 Time building geometry restraints manager: 6.21 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: 0.05 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 58.490 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (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 TRP 0.007 0.001 TRP D 272 HIS 0.002 0.001 HIS A 683 PHE 0.011 0.001 PHE C 266 TYR 0.011 0.001 TYR D 143 ARG 0.001 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.29830 ( 1138) hydrogen bonds : angle 6.77727 ( 3231) covalent geometry : bond 0.00181 (20110) covalent geometry : angle 0.40278 (27390) *********************** 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 : 2.016 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: 0.7930 (mtm) REVERT: A 378 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6323 (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: 0.7197 (t0) REVERT: A 563 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7695 (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: 0.8910 (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: 0.7948 (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: 0.8072 (ptpt) REVERT: B 569 ARG cc_start: 0.8391 (ptp90) cc_final: 0.8137 (ptt-90) REVERT: C 156 TYR cc_start: 0.8231 (t80) cc_final: 0.7681 (t80) 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: 0.7158 (t0) REVERT: C 563 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8401 (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: 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: 0.8313 (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: 0.8189 (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: 0.3399 time to fit residues: 150.3904 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 : 2.355 ------------------------------------------------------------------------------- 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 221 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 683 HIS D 247 GLN D 348 ASN D 445 HIS D 469 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.100591 restraints weight = 50414.427| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.22 r_work: 0.3225 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1681 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= 0.150 Angle : 0.554 6.921 27390 Z= 0.295 Chirality : 0.041 0.221 3218 Planarity : 0.004 0.043 3454 Dihedral : 4.159 58.849 2897 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 1.47 % Allowed : 11.00 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2616 helix: 1.16 (0.13), residues: 1602 sheet: 1.35 (0.48), residues: 102 loop : -0.34 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 272 HIS 0.005 0.001 HIS C 363 PHE 0.018 0.002 PHE B 336 TYR 0.020 0.001 TYR D 593 ARG 0.011 0.001 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.07090 ( 1138) hydrogen bonds : angle 4.52231 ( 3231) covalent geometry : bond 0.00312 (20110) covalent geometry : angle 0.55444 (27390) *********************** 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 264 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 2.023 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 422 GLU cc_start: 0.8421 (pt0) cc_final: 0.7944 (pp20) REVERT: A 539 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7613 (t80) REVERT: A 543 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8019 (mttp) REVERT: A 563 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8292 (tp-100) REVERT: A 672 ASN cc_start: 0.7847 (m110) cc_final: 0.7550 (p0) REVERT: A 678 HIS cc_start: 0.7400 (t-90) cc_final: 0.7193 (t-90) REVERT: A 696 GLN cc_start: 0.8767 (mt0) cc_final: 0.8338 (mt0) REVERT: B 225 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8001 (pt0) REVERT: B 227 TYR cc_start: 0.9197 (t80) cc_final: 0.8979 (t80) REVERT: B 347 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7812 (mtp) REVERT: B 365 ARG cc_start: 0.8946 (mmm160) cc_final: 0.8467 (tpt90) REVERT: B 405 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7068 (mtm-85) REVERT: B 432 GLU cc_start: 0.8819 (pt0) cc_final: 0.8481 (pm20) REVERT: B 558 TYR cc_start: 0.8297 (m-80) cc_final: 0.7890 (m-80) REVERT: B 565 LYS cc_start: 0.8912 (mttp) cc_final: 0.8169 (ptpp) REVERT: B 569 ARG cc_start: 0.8673 (ptp90) cc_final: 0.8258 (ptt-90) REVERT: C 205 MET cc_start: 0.8718 (ttp) cc_final: 0.8444 (ttm) REVERT: C 378 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6594 (mm) REVERT: C 560 ASP cc_start: 0.7636 (t0) cc_final: 0.7335 (t0) REVERT: C 563 GLN cc_start: 0.8978 (tp40) cc_final: 0.8542 (tp-100) REVERT: C 672 ASN cc_start: 0.8316 (m-40) cc_final: 0.8091 (p0) REVERT: D 147 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7489 (t80) REVERT: D 365 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8551 (tpt90) REVERT: D 405 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6874 (mtm-85) REVERT: D 432 GLU cc_start: 0.8803 (pt0) cc_final: 0.8467 (pm20) REVERT: D 558 TYR cc_start: 0.8158 (m-80) cc_final: 0.7861 (m-80) outliers start: 25 outliers final: 12 residues processed: 256 average time/residue: 0.3213 time to fit residues: 123.8370 Evaluate side-chains 220 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 347 MET 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 498 ASP Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 650 CYS Chi-restraints excluded: chain C residue 661 LEU 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 209 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 238 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 667 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.169177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103367 restraints weight = 44886.153| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.34 r_work: 0.3272 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20110 Z= 0.125 Angle : 0.520 8.280 27390 Z= 0.270 Chirality : 0.040 0.177 3218 Planarity : 0.004 0.042 3454 Dihedral : 3.927 59.690 2891 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 1.63 % Allowed : 12.64 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2616 helix: 1.49 (0.13), residues: 1598 sheet: 1.31 (0.48), residues: 102 loop : -0.46 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 272 HIS 0.007 0.001 HIS A 445 PHE 0.025 0.001 PHE B 336 TYR 0.016 0.001 TYR B 593 ARG 0.007 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 1138) hydrogen bonds : angle 3.97542 ( 3231) covalent geometry : bond 0.00268 (20110) covalent geometry : angle 0.52007 (27390) *********************** 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 257 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 2.037 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: 0.7819 (t80) cc_final: 0.7370 (t80) REVERT: A 378 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6230 (mm) REVERT: A 422 GLU cc_start: 0.8290 (pt0) cc_final: 0.7766 (pp20) REVERT: A 563 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8290 (tp-100) REVERT: A 650 CYS cc_start: 0.8320 (p) cc_final: 0.7719 (p) REVERT: A 667 ASN cc_start: 0.8476 (m-40) cc_final: 0.8195 (m110) REVERT: A 672 ASN cc_start: 0.7852 (m110) cc_final: 0.7546 (p0) REVERT: A 678 HIS cc_start: 0.7413 (t-90) cc_final: 0.7196 (t-90) REVERT: A 696 GLN cc_start: 0.8887 (mt0) cc_final: 0.8477 (mt0) REVERT: B 225 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8041 (pt0) REVERT: B 365 ARG cc_start: 0.8978 (mmm160) cc_final: 0.8456 (tpt90) REVERT: B 405 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.7121 (mtm-85) REVERT: B 432 GLU cc_start: 0.8773 (pt0) cc_final: 0.8440 (pm20) REVERT: B 558 TYR cc_start: 0.8145 (m-80) cc_final: 0.7829 (m-80) REVERT: B 569 ARG cc_start: 0.8736 (ptp90) cc_final: 0.8412 (ptt-90) REVERT: C 156 TYR cc_start: 0.7814 (t80) cc_final: 0.7359 (t80) REVERT: C 323 MET cc_start: 0.8996 (tpp) cc_final: 0.8794 (mmm) REVERT: C 378 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6600 (mm) REVERT: C 560 ASP cc_start: 0.7629 (t0) cc_final: 0.7306 (t0) REVERT: C 563 GLN cc_start: 0.8948 (tp40) cc_final: 0.8534 (tp-100) REVERT: C 672 ASN cc_start: 0.8169 (m-40) cc_final: 0.7929 (p0) REVERT: D 147 TYR cc_start: 0.7837 (OUTLIER) cc_final: 0.7477 (t80) REVERT: D 365 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.8612 (tpt90) REVERT: D 432 GLU cc_start: 0.8784 (pt0) cc_final: 0.8454 (pm20) REVERT: D 558 TYR cc_start: 0.7959 (m-80) cc_final: 0.7753 (m-80) outliers start: 28 outliers final: 10 residues processed: 244 average time/residue: 0.3081 time to fit residues: 114.3487 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 : 2.000 ------------------------------------------------------------------------------- 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 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 378 LEU Chi-restraints excluded: chain C residue 498 ASP 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 33 optimal weight: 0.9980 chunk 130 optimal weight: 50.0000 chunk 82 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 150 optimal weight: 0.0870 chunk 119 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.170089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.109115 restraints weight = 55338.663| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.28 r_work: 0.3229 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20110 Z= 0.109 Angle : 0.503 9.521 27390 Z= 0.257 Chirality : 0.040 0.155 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.856 59.540 2889 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 1.80 % Allowed : 12.96 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2616 helix: 1.74 (0.13), residues: 1600 sheet: 1.64 (0.48), residues: 98 loop : -0.53 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 272 HIS 0.011 0.001 HIS C 678 PHE 0.028 0.001 PHE B 336 TYR 0.024 0.001 TYR A 599 ARG 0.007 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 1138) hydrogen bonds : angle 3.70731 ( 3231) covalent geometry : bond 0.00232 (20110) covalent geometry : angle 0.50340 (27390) *********************** 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 268 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 2.241 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: 0.7647 (t80) cc_final: 0.7235 (t80) REVERT: A 378 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6168 (mm) REVERT: A 422 GLU cc_start: 0.8042 (pt0) cc_final: 0.7755 (pp20) REVERT: A 563 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8214 (tp-100) REVERT: A 650 CYS cc_start: 0.8340 (p) cc_final: 0.7756 (p) REVERT: A 672 ASN cc_start: 0.7792 (m110) cc_final: 0.7432 (p0) REVERT: A 678 HIS cc_start: 0.7389 (t-90) cc_final: 0.7140 (t-90) REVERT: A 696 GLN cc_start: 0.8916 (mt0) cc_final: 0.8475 (mt0) REVERT: B 365 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8507 (tpt90) REVERT: B 405 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6994 (mtm-85) REVERT: B 432 GLU cc_start: 0.8583 (pt0) cc_final: 0.8255 (pm20) REVERT: B 438 ASP cc_start: 0.8416 (p0) cc_final: 0.8174 (p0) REVERT: B 558 TYR cc_start: 0.8082 (m-80) cc_final: 0.7874 (m-80) REVERT: C 156 TYR cc_start: 0.7636 (t80) cc_final: 0.7216 (t80) REVERT: C 378 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6591 (mm) REVERT: C 563 GLN cc_start: 0.8917 (tp40) cc_final: 0.8444 (tp-100) REVERT: C 593 TYR cc_start: 0.7672 (m-10) cc_final: 0.7103 (m-10) REVERT: C 672 ASN cc_start: 0.8120 (m-40) cc_final: 0.7813 (p0) REVERT: D 147 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7260 (t80) REVERT: D 169 MET cc_start: 0.8230 (mmm) cc_final: 0.8014 (mmm) REVERT: D 365 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8633 (tpt90) REVERT: D 432 GLU cc_start: 0.8608 (pt0) cc_final: 0.8292 (pm20) outliers start: 31 outliers final: 16 residues processed: 254 average time/residue: 0.3285 time to fit residues: 127.9375 Evaluate side-chains 226 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP 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 491 LEU Chi-restraints excluded: chain C residue 129 ILE 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 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 211 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 363 HIS C 445 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.168988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108003 restraints weight = 54311.282| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.59 r_work: 0.3235 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20110 Z= 0.123 Angle : 0.530 10.687 27390 Z= 0.267 Chirality : 0.040 0.191 3218 Planarity : 0.003 0.040 3454 Dihedral : 3.874 59.736 2889 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 1.63 % Allowed : 13.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.17), residues: 2616 helix: 1.84 (0.13), residues: 1606 sheet: 1.66 (0.49), residues: 98 loop : -0.51 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 272 HIS 0.013 0.001 HIS C 678 PHE 0.018 0.001 PHE B 336 TYR 0.023 0.001 TYR B 593 ARG 0.007 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 1138) hydrogen bonds : angle 3.68706 ( 3231) covalent geometry : bond 0.00278 (20110) covalent geometry : angle 0.52957 (27390) *********************** 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 237 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 2.018 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: 0.7699 (t80) cc_final: 0.7305 (t80) REVERT: A 378 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6178 (mm) REVERT: A 563 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8257 (tp-100) REVERT: A 650 CYS cc_start: 0.8298 (p) cc_final: 0.7688 (p) REVERT: A 672 ASN cc_start: 0.7631 (m110) cc_final: 0.7251 (p0) REVERT: A 678 HIS cc_start: 0.7497 (t-90) cc_final: 0.7254 (t-90) REVERT: A 696 GLN cc_start: 0.8901 (mt0) cc_final: 0.8448 (mt0) REVERT: B 365 ARG cc_start: 0.8976 (mmm160) cc_final: 0.8585 (tpt90) REVERT: B 432 GLU cc_start: 0.8591 (pt0) cc_final: 0.8280 (pm20) REVERT: B 438 ASP cc_start: 0.8431 (p0) cc_final: 0.8176 (p0) REVERT: B 558 TYR cc_start: 0.8140 (m-80) cc_final: 0.7928 (m-80) REVERT: C 156 TYR cc_start: 0.7699 (t80) cc_final: 0.7291 (t80) REVERT: C 378 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6588 (mm) REVERT: C 563 GLN cc_start: 0.8934 (tp40) cc_final: 0.8460 (tp-100) REVERT: C 593 TYR cc_start: 0.7776 (m-10) cc_final: 0.7098 (m-10) REVERT: C 672 ASN cc_start: 0.8090 (m-40) cc_final: 0.7756 (p0) REVERT: D 147 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7349 (t80) REVERT: D 169 MET cc_start: 0.8339 (mmm) cc_final: 0.8102 (mmm) REVERT: D 344 MET cc_start: 0.8810 (mmm) cc_final: 0.8456 (mmm) REVERT: D 365 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8581 (tpt90) REVERT: D 432 GLU cc_start: 0.8596 (pt0) cc_final: 0.8297 (pm20) outliers start: 28 outliers final: 17 residues processed: 226 average time/residue: 0.2996 time to fit residues: 104.4731 Evaluate side-chains 219 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 2.016 ------------------------------------------------------------------------------- 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 548 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 129 ILE 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 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 49 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 170 optimal weight: 0.0060 chunk 85 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 220 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.168070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.110327 restraints weight = 60983.186| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.71 r_work: 0.3148 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20110 Z= 0.135 Angle : 0.537 9.460 27390 Z= 0.273 Chirality : 0.041 0.157 3218 Planarity : 0.003 0.040 3454 Dihedral : 3.925 59.372 2889 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 14.27 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2616 helix: 1.92 (0.13), residues: 1592 sheet: 1.87 (0.49), residues: 94 loop : -0.55 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 272 HIS 0.014 0.001 HIS C 678 PHE 0.031 0.001 PHE B 336 TYR 0.015 0.001 TYR C 280 ARG 0.008 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1138) hydrogen bonds : angle 3.67340 ( 3231) covalent geometry : bond 0.00309 (20110) covalent geometry : angle 0.53748 (27390) *********************** 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 241 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 2.213 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: 0.7722 (t80) cc_final: 0.7308 (t80) REVERT: A 378 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6164 (mm) REVERT: A 422 GLU cc_start: 0.8210 (pt0) cc_final: 0.7735 (pp20) REVERT: A 650 CYS cc_start: 0.8324 (p) cc_final: 0.7707 (p) REVERT: A 672 ASN cc_start: 0.7576 (m110) cc_final: 0.7179 (p0) REVERT: A 696 GLN cc_start: 0.8911 (mt0) cc_final: 0.8512 (mt0) REVERT: B 344 MET cc_start: 0.8821 (tpp) cc_final: 0.8478 (mmm) REVERT: B 365 ARG cc_start: 0.9005 (mmm160) cc_final: 0.8587 (tpt90) REVERT: B 428 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8244 (mm-30) REVERT: B 432 GLU cc_start: 0.8611 (pt0) cc_final: 0.8279 (pm20) REVERT: B 438 ASP cc_start: 0.8492 (p0) cc_final: 0.8218 (p0) REVERT: C 156 TYR cc_start: 0.7724 (t80) cc_final: 0.7294 (t80) REVERT: C 378 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6615 (mm) REVERT: C 563 GLN cc_start: 0.8972 (tp40) cc_final: 0.8474 (tp-100) REVERT: C 643 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7648 (tp30) REVERT: C 696 GLN cc_start: 0.8593 (mp10) cc_final: 0.8343 (mp10) REVERT: D 147 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7455 (t80) REVERT: D 169 MET cc_start: 0.8464 (mmm) cc_final: 0.8189 (mmm) REVERT: D 344 MET cc_start: 0.8806 (mmm) cc_final: 0.8500 (mmm) REVERT: D 365 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8638 (tpt90) REVERT: D 432 GLU cc_start: 0.8616 (pt0) cc_final: 0.8296 (pm20) REVERT: D 558 TYR cc_start: 0.7685 (m-80) cc_final: 0.7405 (m-80) outliers start: 28 outliers final: 21 residues processed: 229 average time/residue: 0.3204 time to fit residues: 113.6069 Evaluate side-chains 230 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 2.367 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain B residue 205 MET 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 B residue 664 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL 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 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 299 MET 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 10 optimal weight: 0.0050 chunk 218 optimal weight: 0.8980 chunk 245 optimal weight: 0.0980 chunk 49 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 260 optimal weight: 50.0000 chunk 238 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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** D 500 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.169363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109949 restraints weight = 61205.387| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 4.27 r_work: 0.3185 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 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 = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20110 Z= 0.110 Angle : 0.520 9.265 27390 Z= 0.264 Chirality : 0.040 0.160 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.877 59.973 2889 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 1.63 % Allowed : 14.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2616 helix: 1.96 (0.13), residues: 1608 sheet: 1.81 (0.48), residues: 94 loop : -0.48 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 272 HIS 0.015 0.001 HIS C 678 PHE 0.017 0.001 PHE D 336 TYR 0.029 0.001 TYR C 599 ARG 0.008 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1138) hydrogen bonds : angle 3.57723 ( 3231) covalent geometry : bond 0.00237 (20110) covalent geometry : angle 0.52021 (27390) *********************** 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 247 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 2.017 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: 0.7650 (t80) cc_final: 0.7259 (t80) REVERT: A 378 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6091 (mm) REVERT: A 422 GLU cc_start: 0.8087 (pt0) cc_final: 0.7684 (pp20) REVERT: A 603 GLU cc_start: 0.8354 (tp30) cc_final: 0.7845 (tp30) REVERT: A 672 ASN cc_start: 0.7684 (m110) cc_final: 0.7244 (p0) REVERT: A 696 GLN cc_start: 0.8920 (mt0) cc_final: 0.8522 (mt0) REVERT: B 344 MET cc_start: 0.8812 (tpp) cc_final: 0.8459 (mmm) REVERT: B 365 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8562 (tpt90) REVERT: B 428 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8265 (mm-30) REVERT: B 432 GLU cc_start: 0.8674 (pt0) cc_final: 0.8341 (pm20) REVERT: B 438 ASP cc_start: 0.8457 (p0) cc_final: 0.8164 (p0) REVERT: B 476 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 649 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7546 (tt) REVERT: C 156 TYR cc_start: 0.7684 (t80) cc_final: 0.7264 (t80) REVERT: C 378 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6584 (mm) REVERT: C 563 GLN cc_start: 0.8987 (tp40) cc_final: 0.8514 (tp-100) REVERT: C 593 TYR cc_start: 0.7811 (m-10) cc_final: 0.7135 (m-10) REVERT: C 696 GLN cc_start: 0.8471 (mp10) cc_final: 0.8234 (mp10) REVERT: D 147 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7261 (t80) REVERT: D 344 MET cc_start: 0.8833 (mmm) cc_final: 0.8580 (mmm) REVERT: D 365 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8532 (tpt90) REVERT: D 432 GLU cc_start: 0.8677 (pt0) cc_final: 0.8356 (pm20) REVERT: D 558 TYR cc_start: 0.7649 (m-80) cc_final: 0.7366 (m-80) outliers start: 28 outliers final: 19 residues processed: 236 average time/residue: 0.3052 time to fit residues: 110.7140 Evaluate side-chains 235 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 2.089 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 476 ILE 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 129 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL 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 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 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 203 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 149 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.168631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.109833 restraints weight = 65828.334| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 4.79 r_work: 0.3151 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20110 Z= 0.123 Angle : 0.535 11.674 27390 Z= 0.269 Chirality : 0.040 0.155 3218 Planarity : 0.003 0.041 3454 Dihedral : 3.867 59.595 2889 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.02 % Favored : 95.90 % Rotamer: Outliers : 1.63 % Allowed : 14.65 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2616 helix: 2.03 (0.13), residues: 1606 sheet: 1.76 (0.48), residues: 94 loop : -0.50 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 272 HIS 0.016 0.001 HIS C 678 PHE 0.018 0.001 PHE B 336 TYR 0.015 0.001 TYR C 280 ARG 0.008 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1138) hydrogen bonds : angle 3.54938 ( 3231) covalent geometry : bond 0.00279 (20110) covalent geometry : angle 0.53491 (27390) *********************** 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 244 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 2.027 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: 0.7658 (t80) cc_final: 0.7253 (t80) REVERT: A 378 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6099 (mm) REVERT: A 422 GLU cc_start: 0.8106 (pt0) cc_final: 0.7709 (pp20) REVERT: A 672 ASN cc_start: 0.7714 (m110) cc_final: 0.7262 (p0) REVERT: A 696 GLN cc_start: 0.8947 (mt0) cc_final: 0.8586 (mt0) REVERT: B 344 MET cc_start: 0.8817 (tpp) cc_final: 0.8456 (mmm) REVERT: B 365 ARG cc_start: 0.8974 (mmm160) cc_final: 0.8568 (tpt90) REVERT: B 428 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 432 GLU cc_start: 0.8718 (pt0) cc_final: 0.8393 (pm20) REVERT: B 438 ASP cc_start: 0.8476 (p0) cc_final: 0.8155 (p0) REVERT: B 476 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8166 (mt) REVERT: B 649 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7512 (tt) REVERT: C 156 TYR cc_start: 0.7668 (t80) cc_final: 0.7243 (t80) REVERT: C 378 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6573 (mm) REVERT: C 563 GLN cc_start: 0.8978 (tp40) cc_final: 0.8470 (tp-100) REVERT: C 593 TYR cc_start: 0.7794 (m-10) cc_final: 0.7078 (m-10) REVERT: C 606 ASP cc_start: 0.8806 (t0) cc_final: 0.8478 (t0) REVERT: D 147 TYR cc_start: 0.7880 (OUTLIER) cc_final: 0.7328 (t80) REVERT: D 344 MET cc_start: 0.8790 (mmm) cc_final: 0.8535 (mmm) REVERT: D 365 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8625 (tpt90) REVERT: D 432 GLU cc_start: 0.8704 (pt0) cc_final: 0.8391 (pm20) REVERT: D 558 TYR cc_start: 0.7634 (m-80) cc_final: 0.7371 (m-80) outliers start: 28 outliers final: 21 residues processed: 232 average time/residue: 0.3045 time to fit residues: 109.8863 Evaluate side-chains 235 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 LEU 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 476 ILE 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 129 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL 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 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 299 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 203 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 223 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 220 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS ** B 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.169794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103272 restraints weight = 46991.964| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.12 r_work: 0.3258 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20110 Z= 0.106 Angle : 0.530 11.165 27390 Z= 0.264 Chirality : 0.040 0.175 3218 Planarity : 0.003 0.042 3454 Dihedral : 3.840 59.923 2889 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.94 % Favored : 95.98 % Rotamer: Outliers : 1.58 % Allowed : 14.71 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.17), residues: 2616 helix: 2.08 (0.13), residues: 1606 sheet: 1.71 (0.47), residues: 94 loop : -0.50 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 272 HIS 0.016 0.001 HIS C 678 PHE 0.018 0.001 PHE B 336 TYR 0.013 0.001 TYR A 280 ARG 0.008 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 1138) hydrogen bonds : angle 3.45826 ( 3231) covalent geometry : bond 0.00228 (20110) covalent geometry : angle 0.52991 (27390) *********************** 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 244 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 2.061 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: 0.7615 (t80) cc_final: 0.7227 (t80) REVERT: A 378 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6047 (mm) REVERT: A 422 GLU cc_start: 0.8123 (pt0) cc_final: 0.7717 (pp20) REVERT: A 672 ASN cc_start: 0.7795 (m110) cc_final: 0.7271 (p0) REVERT: A 696 GLN cc_start: 0.8895 (mt0) cc_final: 0.8646 (mt0) REVERT: B 365 ARG cc_start: 0.8989 (mmm160) cc_final: 0.8500 (tpt90) REVERT: B 428 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 432 GLU cc_start: 0.8776 (pt0) cc_final: 0.8436 (pm20) REVERT: B 438 ASP cc_start: 0.8509 (p0) cc_final: 0.8190 (p0) REVERT: B 476 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8148 (mt) REVERT: B 649 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7486 (tt) REVERT: C 156 TYR cc_start: 0.7620 (t80) cc_final: 0.7209 (t80) REVERT: C 378 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6479 (mm) REVERT: C 563 GLN cc_start: 0.8984 (tp40) cc_final: 0.8496 (tp-100) REVERT: C 606 ASP cc_start: 0.8801 (t0) cc_final: 0.8475 (t0) REVERT: C 655 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8507 (mmmm) REVERT: D 147 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7246 (t80) REVERT: D 344 MET cc_start: 0.8814 (mmm) cc_final: 0.8590 (mmm) REVERT: D 365 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8543 (tpt90) REVERT: D 432 GLU cc_start: 0.8769 (pt0) cc_final: 0.8441 (pm20) REVERT: D 558 TYR cc_start: 0.7638 (m-80) cc_final: 0.7385 (m-80) outliers start: 27 outliers final: 20 residues processed: 235 average time/residue: 0.3084 time to fit residues: 112.7224 Evaluate side-chains 233 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 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 C residue 129 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL 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 C residue 661 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 197 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.168404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101334 restraints weight = 48705.399| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.19 r_work: 0.3269 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20110 Z= 0.132 Angle : 0.550 11.685 27390 Z= 0.277 Chirality : 0.041 0.171 3218 Planarity : 0.003 0.042 3454 Dihedral : 3.895 59.937 2889 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 1.53 % Allowed : 14.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2616 helix: 2.06 (0.13), residues: 1606 sheet: 1.70 (0.48), residues: 94 loop : -0.50 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 272 HIS 0.017 0.001 HIS C 678 PHE 0.028 0.001 PHE B 336 TYR 0.015 0.001 TYR B 280 ARG 0.008 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1138) hydrogen bonds : angle 3.51755 ( 3231) covalent geometry : bond 0.00305 (20110) covalent geometry : angle 0.55020 (27390) ********************** 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 236 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 2.174 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: 0.7729 (t80) cc_final: 0.7337 (t80) REVERT: A 378 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6085 (mm) REVERT: A 422 GLU cc_start: 0.8175 (pt0) cc_final: 0.7759 (pp20) REVERT: A 672 ASN cc_start: 0.7801 (m110) cc_final: 0.7268 (p0) REVERT: A 696 GLN cc_start: 0.8839 (mt0) cc_final: 0.8605 (mt0) REVERT: B 344 MET cc_start: 0.8850 (tpp) cc_final: 0.8513 (mmm) REVERT: B 365 ARG cc_start: 0.9014 (mmm160) cc_final: 0.8574 (tpt90) REVERT: B 428 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8226 (mm-30) REVERT: B 432 GLU cc_start: 0.8802 (pt0) cc_final: 0.8474 (pm20) REVERT: B 438 ASP cc_start: 0.8502 (p0) cc_final: 0.8184 (p0) REVERT: B 476 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 569 ARG cc_start: 0.8758 (ptp90) cc_final: 0.8494 (ptt-90) REVERT: B 649 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7567 (tt) REVERT: C 156 TYR cc_start: 0.7718 (t80) cc_final: 0.7310 (t80) REVERT: C 378 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6512 (mm) REVERT: C 563 GLN cc_start: 0.8992 (tp40) cc_final: 0.8486 (tp-100) REVERT: C 606 ASP cc_start: 0.8814 (t0) cc_final: 0.8437 (t0) REVERT: C 655 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8499 (mmmm) REVERT: D 147 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7377 (t80) REVERT: D 344 MET cc_start: 0.8824 (mmm) cc_final: 0.8599 (mmm) REVERT: D 365 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8523 (tpt90) REVERT: D 432 GLU cc_start: 0.8796 (pt0) cc_final: 0.8475 (pm20) REVERT: D 558 TYR cc_start: 0.7650 (m-80) cc_final: 0.7440 (m-80) outliers start: 26 outliers final: 21 residues processed: 226 average time/residue: 0.3002 time to fit residues: 105.5921 Evaluate side-chains 234 residues out of total 2290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 447 VAL Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 550 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 C residue 129 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 447 VAL 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 C residue 661 LEU 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 Chi-restraints excluded: chain D residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 GLN ** C 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.167957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107225 restraints weight = 51843.238| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.05 r_work: 0.3174 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 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 = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20110 Z= 0.136 Angle : 0.555 11.736 27390 Z= 0.279 Chirality : 0.041 0.165 3218 Planarity : 0.003 0.042 3454 Dihedral : 3.930 59.690 2889 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.63 % Allowed : 14.98 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2616 helix: 2.03 (0.13), residues: 1610 sheet: 1.71 (0.48), residues: 94 loop : -0.48 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 272 HIS 0.017 0.001 HIS C 678 PHE 0.018 0.001 PHE D 336 TYR 0.015 0.001 TYR D 280 ARG 0.008 0.000 ARG C 487 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1138) hydrogen bonds : angle 3.52987 ( 3231) covalent geometry : bond 0.00316 (20110) covalent geometry : angle 0.55506 (27390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14100.22 seconds wall clock time: 243 minutes 26.76 seconds (14606.76 seconds total)