Starting phenix.real_space_refine on Sat Feb 7 07:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh7_63088/02_2026/9lh7_63088.map" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 56 5.16 5 C 19109 2.51 5 N 5285 2.21 5 O 6105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30555 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4371 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 2, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "N" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4364 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 7, 'TYR:plan': 3, 'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Time building chain proxies: 7.18, per 1000 atoms: 0.23 Number of scatterers: 30555 At special positions: 0 Unit cell: (154.56, 152.72, 144.44, 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 56 16.00 O 6105 8.00 N 5285 7.00 C 19109 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 175 " distance=2.44 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 175 " distance=2.44 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 175 " distance=2.44 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 175 " distance=2.44 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 175 " distance=2.44 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 175 " distance=2.44 Simple disulfide: pdb=" SG CYS N 157 " - pdb=" SG CYS N 175 " distance=2.45 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7476 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 106 sheets defined 4.3% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.646A pdb=" N LEU A 354 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.907A pdb=" N GLY A 457 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 530 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.646A pdb=" N LEU B 354 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.908A pdb=" N GLY B 457 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 530 Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.645A pdb=" N LEU C 354 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR C 378 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.909A pdb=" N GLY C 457 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 530 Processing helix chain 'D' and resid 154 through 156 No H-bonds generated for 'chain 'D' and resid 154 through 156' Processing helix chain 'D' and resid 349 through 354 removed outlier: 3.645A pdb=" N LEU D 354 " --> pdb=" O GLU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.907A pdb=" N GLY D 457 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 530 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 349 through 354 removed outlier: 3.644A pdb=" N LEU E 354 " --> pdb=" O GLU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.772A pdb=" N TYR E 378 " --> pdb=" O SER E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 457 removed outlier: 3.909A pdb=" N GLY E 457 " --> pdb=" O VAL E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 530 Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 349 through 354 removed outlier: 3.645A pdb=" N LEU F 354 " --> pdb=" O GLU F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR F 378 " --> pdb=" O SER F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 removed outlier: 3.907A pdb=" N GLY F 457 " --> pdb=" O VAL F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 530 Processing helix chain 'N' and resid 154 through 156 No H-bonds generated for 'chain 'N' and resid 154 through 156' Processing helix chain 'N' and resid 349 through 354 removed outlier: 3.645A pdb=" N LEU N 354 " --> pdb=" O GLU N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 379 removed outlier: 3.774A pdb=" N TYR N 378 " --> pdb=" O SER N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 452 through 457 removed outlier: 3.908A pdb=" N GLY N 457 " --> pdb=" O VAL N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 527 through 530 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.506A pdb=" N GLU A 189 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 205 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP A 386 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR A 270 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 388 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151 removed outlier: 4.016A pdb=" N ILE A 146 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 182 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 180 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE A 183 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 217 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 removed outlier: 3.781A pdb=" N PHE A 159 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 231 removed outlier: 3.653A pdb=" N ARG A 229 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 246 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR A 241 " --> pdb=" O LYS A 418 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 418 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 243 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 416 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 414 " --> pdb=" O TRP A 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 428 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.526A pdb=" N ASN A 343 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.526A pdb=" N ASN A 343 " --> pdb=" O ARG A 327 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 338 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 344 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLN A 252 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA A 251 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG A 410 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP A 253 " --> pdb=" O ASN A 408 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 399 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 448 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 401 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 446 " --> pdb=" O PHE A 401 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 296 removed outlier: 3.503A pdb=" N GLN A 315 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER N 286 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN N 315 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER F 286 " --> pdb=" O ARG N 317 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER E 286 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D 286 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 315 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 286 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 315 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 286 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 315 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 286 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 464 through 465 removed outlier: 3.764A pdb=" N ILE A 574 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 472 through 475 Processing sheet with id=AB1, first strand: chain 'A' and resid 495 through 497 Processing sheet with id=AB2, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AB3, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AB4, first strand: chain 'A' and resid 559 through 562 Processing sheet with id=AB5, first strand: chain 'A' and resid 590 through 591 removed outlier: 6.066A pdb=" N TRP A 702 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL A 711 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS A 700 " --> pdb=" O VAL A 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE A 713 " --> pdb=" O GLN A 698 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN A 698 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU A 619 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.509A pdb=" N ALA A 661 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 688 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA A 647 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 686 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 651 " --> pdb=" O ASN A 682 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A 682 " --> pdb=" O ASP A 651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.506A pdb=" N GLU B 189 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS B 205 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP B 386 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR B 270 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 388 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.015A pdb=" N ILE B 146 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 182 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 180 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 183 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 217 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.780A pdb=" N PHE B 159 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 228 through 231 removed outlier: 3.653A pdb=" N ARG B 229 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 246 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR B 241 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B 418 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG B 243 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 416 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 414 " --> pdb=" O TRP B 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 428 " --> pdb=" O TYR B 417 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN B 343 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN B 343 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 338 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG B 344 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLN B 252 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA B 251 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG B 410 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP B 253 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 399 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 448 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 401 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 446 " --> pdb=" O PHE B 401 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 464 through 465 removed outlier: 3.766A pdb=" N ILE B 574 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 472 through 475 Processing sheet with id=AC7, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AC8, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AC9, first strand: chain 'B' and resid 532 through 534 Processing sheet with id=AD1, first strand: chain 'B' and resid 559 through 562 Processing sheet with id=AD2, first strand: chain 'B' and resid 590 through 591 removed outlier: 6.067A pdb=" N TRP B 702 " --> pdb=" O LYS B 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 711 " --> pdb=" O LYS B 700 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS B 700 " --> pdb=" O VAL B 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE B 713 " --> pdb=" O GLN B 698 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN B 698 " --> pdb=" O PHE B 713 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU B 619 " --> pdb=" O VAL B 627 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.509A pdb=" N ALA B 661 " --> pdb=" O THR B 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 688 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 647 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 651 " --> pdb=" O ASN B 682 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN B 682 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.507A pdb=" N GLU C 189 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS C 205 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 386 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR C 270 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 388 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.016A pdb=" N ILE C 146 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 182 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 180 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 183 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 217 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 158 through 160 removed outlier: 3.779A pdb=" N PHE C 159 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG C 172 " --> pdb=" O PHE C 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 228 through 231 removed outlier: 3.652A pdb=" N ARG C 229 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 246 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR C 241 " --> pdb=" O LYS C 418 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS C 418 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG C 243 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 416 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 414 " --> pdb=" O TRP C 245 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 428 " --> pdb=" O TYR C 417 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.526A pdb=" N ASN C 343 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 326 through 328 removed outlier: 3.526A pdb=" N ASN C 343 " --> pdb=" O ARG C 327 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL C 338 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 344 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N GLN C 252 " --> pdb=" O ARG C 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA C 251 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG C 410 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP C 253 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 399 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 448 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 401 " --> pdb=" O PHE C 446 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE C 446 " --> pdb=" O PHE C 401 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 464 through 465 removed outlier: 3.765A pdb=" N ILE C 574 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 472 through 475 Processing sheet with id=AE4, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AE5, first strand: chain 'C' and resid 511 through 512 Processing sheet with id=AE6, first strand: chain 'C' and resid 532 through 534 Processing sheet with id=AE7, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AE8, first strand: chain 'C' and resid 590 through 591 removed outlier: 6.066A pdb=" N TRP C 702 " --> pdb=" O LYS C 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL C 711 " --> pdb=" O LYS C 700 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS C 700 " --> pdb=" O VAL C 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE C 713 " --> pdb=" O GLN C 698 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN C 698 " --> pdb=" O PHE C 713 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU C 619 " --> pdb=" O VAL C 627 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 671 through 674 removed outlier: 3.511A pdb=" N ALA C 661 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 688 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 647 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 651 " --> pdb=" O ASN C 682 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN C 682 " --> pdb=" O ASP C 651 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.507A pdb=" N GLU D 189 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 205 " --> pdb=" O ALA D 391 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP D 386 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR D 270 " --> pdb=" O ASP D 386 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE D 388 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 146 through 151 removed outlier: 4.014A pdb=" N ILE D 146 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 182 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 180 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 183 " --> pdb=" O GLY D 217 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY D 217 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 158 through 160 removed outlier: 3.781A pdb=" N PHE D 159 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 228 through 231 removed outlier: 3.653A pdb=" N ARG D 229 " --> pdb=" O SER D 246 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 246 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR D 241 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS D 418 " --> pdb=" O TYR D 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG D 243 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 416 " --> pdb=" O ARG D 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 414 " --> pdb=" O TRP D 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 428 " --> pdb=" O TYR D 417 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN D 343 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN D 343 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL D 338 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 344 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLN D 252 " --> pdb=" O ARG D 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA D 251 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG D 410 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP D 253 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 399 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 448 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 401 " --> pdb=" O PHE D 446 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE D 446 " --> pdb=" O PHE D 401 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 464 through 465 removed outlier: 3.764A pdb=" N ILE D 574 " --> pdb=" O GLN D 464 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 472 through 475 Processing sheet with id=AG1, first strand: chain 'D' and resid 495 through 497 Processing sheet with id=AG2, first strand: chain 'D' and resid 511 through 512 Processing sheet with id=AG3, first strand: chain 'D' and resid 532 through 534 Processing sheet with id=AG4, first strand: chain 'D' and resid 559 through 562 Processing sheet with id=AG5, first strand: chain 'D' and resid 590 through 591 removed outlier: 6.067A pdb=" N TRP D 702 " --> pdb=" O LYS D 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 711 " --> pdb=" O LYS D 700 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS D 700 " --> pdb=" O VAL D 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE D 713 " --> pdb=" O GLN D 698 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLN D 698 " --> pdb=" O PHE D 713 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU D 619 " --> pdb=" O VAL D 627 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 671 through 674 removed outlier: 3.511A pdb=" N ALA D 661 " --> pdb=" O THR D 648 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 688 " --> pdb=" O ILE D 645 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA D 647 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D 651 " --> pdb=" O ASN D 682 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN D 682 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.506A pdb=" N GLU E 189 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS E 205 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP E 386 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR E 270 " --> pdb=" O ASP E 386 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE E 388 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 146 through 151 removed outlier: 4.015A pdb=" N ILE E 146 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 182 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 180 " --> pdb=" O ARG E 150 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE E 183 " --> pdb=" O GLY E 217 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY E 217 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 158 through 160 removed outlier: 3.780A pdb=" N PHE E 159 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG E 172 " --> pdb=" O PHE E 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 228 through 231 removed outlier: 3.653A pdb=" N ARG E 229 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER E 246 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR E 241 " --> pdb=" O LYS E 418 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS E 418 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG E 243 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA E 416 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN E 414 " --> pdb=" O TRP E 245 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE E 428 " --> pdb=" O TYR E 417 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN E 343 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA E 337 " --> pdb=" O LYS E 333 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN E 343 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E 338 " --> pdb=" O PHE E 258 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG E 344 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLN E 252 " --> pdb=" O ARG E 344 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA E 251 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG E 410 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP E 253 " --> pdb=" O ASN E 408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR E 399 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 448 " --> pdb=" O THR E 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE E 401 " --> pdb=" O PHE E 446 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE E 446 " --> pdb=" O PHE E 401 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 464 through 465 removed outlier: 3.765A pdb=" N ILE E 574 " --> pdb=" O GLN E 464 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 472 through 475 Processing sheet with id=AH7, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AH8, first strand: chain 'E' and resid 511 through 512 Processing sheet with id=AH9, first strand: chain 'E' and resid 532 through 534 Processing sheet with id=AI1, first strand: chain 'E' and resid 559 through 562 Processing sheet with id=AI2, first strand: chain 'E' and resid 590 through 591 removed outlier: 6.067A pdb=" N TRP E 702 " --> pdb=" O LYS E 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL E 711 " --> pdb=" O LYS E 700 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS E 700 " --> pdb=" O VAL E 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE E 713 " --> pdb=" O GLN E 698 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN E 698 " --> pdb=" O PHE E 713 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 627 through 628 removed outlier: 3.613A pdb=" N LEU E 619 " --> pdb=" O VAL E 627 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 671 through 674 removed outlier: 3.510A pdb=" N ALA E 661 " --> pdb=" O THR E 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 688 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA E 647 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP E 651 " --> pdb=" O ASN E 682 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN E 682 " --> pdb=" O ASP E 651 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 142 through 143 removed outlier: 3.506A pdb=" N GLU F 189 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS F 205 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP F 386 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR F 270 " --> pdb=" O ASP F 386 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE F 388 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 146 through 151 removed outlier: 4.015A pdb=" N ILE F 146 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 182 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 180 " --> pdb=" O ARG F 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE F 183 " --> pdb=" O GLY F 217 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY F 217 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.780A pdb=" N PHE F 159 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 172 " --> pdb=" O PHE F 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 228 through 231 removed outlier: 3.653A pdb=" N ARG F 229 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER F 246 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR F 241 " --> pdb=" O LYS F 418 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS F 418 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG F 243 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA F 416 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN F 414 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 428 " --> pdb=" O TYR F 417 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 326 through 328 removed outlier: 3.525A pdb=" N ASN F 343 " --> pdb=" O ARG F 327 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA F 337 " --> pdb=" O LYS F 333 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 326 through 328 removed outlier: 3.525A pdb=" N ASN F 343 " --> pdb=" O ARG F 327 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL F 338 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG F 344 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLN F 252 " --> pdb=" O ARG F 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA F 251 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG F 410 " --> pdb=" O ALA F 251 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP F 253 " --> pdb=" O ASN F 408 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 399 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 448 " --> pdb=" O THR F 399 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE F 401 " --> pdb=" O PHE F 446 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE F 446 " --> pdb=" O PHE F 401 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 464 through 465 removed outlier: 3.765A pdb=" N ILE F 574 " --> pdb=" O GLN F 464 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 472 through 475 Processing sheet with id=AJ4, first strand: chain 'F' and resid 495 through 497 Processing sheet with id=AJ5, first strand: chain 'F' and resid 511 through 512 Processing sheet with id=AJ6, first strand: chain 'F' and resid 532 through 534 Processing sheet with id=AJ7, first strand: chain 'F' and resid 559 through 562 Processing sheet with id=AJ8, first strand: chain 'F' and resid 590 through 591 removed outlier: 6.066A pdb=" N TRP F 702 " --> pdb=" O LYS F 709 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL F 711 " --> pdb=" O LYS F 700 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS F 700 " --> pdb=" O VAL F 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE F 713 " --> pdb=" O GLN F 698 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN F 698 " --> pdb=" O PHE F 713 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU F 619 " --> pdb=" O VAL F 627 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 671 through 674 removed outlier: 3.510A pdb=" N ALA F 661 " --> pdb=" O THR F 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE F 688 " --> pdb=" O ILE F 645 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA F 647 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP F 651 " --> pdb=" O ASN F 682 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN F 682 " --> pdb=" O ASP F 651 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'N' and resid 142 through 143 removed outlier: 3.505A pdb=" N GLU N 189 " --> pdb=" O ILE N 206 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS N 205 " --> pdb=" O ALA N 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP N 386 " --> pdb=" O THR N 270 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N THR N 270 " --> pdb=" O ASP N 386 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE N 388 " --> pdb=" O LEU N 268 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'N' and resid 146 through 151 removed outlier: 4.016A pdb=" N ILE N 146 " --> pdb=" O TYR N 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU N 182 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE N 180 " --> pdb=" O ARG N 150 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE N 183 " --> pdb=" O GLY N 217 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY N 217 " --> pdb=" O ILE N 183 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'N' and resid 158 through 160 removed outlier: 3.780A pdb=" N PHE N 159 " --> pdb=" O ARG N 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG N 172 " --> pdb=" O PHE N 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'N' and resid 228 through 231 removed outlier: 3.652A pdb=" N ARG N 229 " --> pdb=" O SER N 246 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER N 246 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR N 241 " --> pdb=" O LYS N 418 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS N 418 " --> pdb=" O TYR N 241 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG N 243 " --> pdb=" O ALA N 416 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA N 416 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN N 414 " --> pdb=" O TRP N 245 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE N 428 " --> pdb=" O TYR N 417 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN N 343 " --> pdb=" O ARG N 327 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA N 337 " --> pdb=" O LYS N 333 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 326 through 328 removed outlier: 3.524A pdb=" N ASN N 343 " --> pdb=" O ARG N 327 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL N 338 " --> pdb=" O PHE N 258 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG N 344 " --> pdb=" O GLN N 252 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N GLN N 252 " --> pdb=" O ARG N 344 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA N 251 " --> pdb=" O ARG N 410 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG N 410 " --> pdb=" O ALA N 251 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP N 253 " --> pdb=" O ASN N 408 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR N 399 " --> pdb=" O VAL N 448 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL N 448 " --> pdb=" O THR N 399 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE N 401 " --> pdb=" O PHE N 446 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE N 446 " --> pdb=" O PHE N 401 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 464 through 465 removed outlier: 3.763A pdb=" N ILE N 574 " --> pdb=" O GLN N 464 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'N' and resid 472 through 475 Processing sheet with id=AL1, first strand: chain 'N' and resid 495 through 497 Processing sheet with id=AL2, first strand: chain 'N' and resid 511 through 512 Processing sheet with id=AL3, first strand: chain 'N' and resid 532 through 534 Processing sheet with id=AL4, first strand: chain 'N' and resid 559 through 562 Processing sheet with id=AL5, first strand: chain 'N' and resid 590 through 591 removed outlier: 6.066A pdb=" N TRP N 702 " --> pdb=" O LYS N 709 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL N 711 " --> pdb=" O LYS N 700 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS N 700 " --> pdb=" O VAL N 711 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N PHE N 713 " --> pdb=" O GLN N 698 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLN N 698 " --> pdb=" O PHE N 713 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'N' and resid 627 through 628 removed outlier: 3.612A pdb=" N LEU N 619 " --> pdb=" O VAL N 627 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 671 through 674 removed outlier: 3.508A pdb=" N ALA N 661 " --> pdb=" O THR N 648 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE N 688 " --> pdb=" O ILE N 645 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA N 647 " --> pdb=" O ASP N 686 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP N 651 " --> pdb=" O ASN N 682 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN N 682 " --> pdb=" O ASP N 651 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2544 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: 7.07 Time building geometry restraints manager: 2.89 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: 10423 1.34 - 1.46: 7687 1.46 - 1.58: 13027 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 31207 Sorted by residual: bond pdb=" CG ARG C 229 " pdb=" CD ARG C 229 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 bond pdb=" CG ARG B 229 " pdb=" CD ARG B 229 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG ARG F 229 " pdb=" CD ARG F 229 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG ARG D 229 " pdb=" CD ARG D 229 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" CG ARG N 229 " pdb=" CD ARG N 229 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 31202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 41370 1.75 - 3.50: 1047 3.50 - 5.25: 147 5.25 - 7.00: 14 7.00 - 8.75: 7 Bond angle restraints: 42585 Sorted by residual: angle pdb=" N VAL B 580 " pdb=" CA VAL B 580 " pdb=" C VAL B 580 " ideal model delta sigma weight residual 111.77 106.08 5.69 1.04e+00 9.25e-01 2.99e+01 angle pdb=" N VAL A 580 " pdb=" CA VAL A 580 " pdb=" C VAL A 580 " ideal model delta sigma weight residual 111.77 106.09 5.68 1.04e+00 9.25e-01 2.98e+01 angle pdb=" N VAL N 580 " pdb=" CA VAL N 580 " pdb=" C VAL N 580 " ideal model delta sigma weight residual 111.77 106.14 5.63 1.04e+00 9.25e-01 2.93e+01 angle pdb=" N VAL F 580 " pdb=" CA VAL F 580 " pdb=" C VAL F 580 " ideal model delta sigma weight residual 111.77 106.14 5.63 1.04e+00 9.25e-01 2.93e+01 angle pdb=" N VAL D 580 " pdb=" CA VAL D 580 " pdb=" C VAL D 580 " ideal model delta sigma weight residual 111.77 106.15 5.62 1.04e+00 9.25e-01 2.92e+01 ... (remaining 42580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 16351 17.00 - 34.00: 1524 34.00 - 51.01: 167 51.01 - 68.01: 49 68.01 - 85.01: 56 Dihedral angle restraints: 18147 sinusoidal: 6477 harmonic: 11670 Sorted by residual: dihedral pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 19.92 73.08 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS F 157 " pdb=" SG CYS F 157 " pdb=" SG CYS F 175 " pdb=" CB CYS F 175 " ideal model delta sinusoidal sigma weight residual 93.00 19.99 73.01 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 175 " pdb=" CB CYS D 175 " ideal model delta sinusoidal sigma weight residual 93.00 20.17 72.83 1 1.00e+01 1.00e-02 6.77e+01 ... (remaining 18144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 3852 0.052 - 0.103: 737 0.103 - 0.155: 143 0.155 - 0.207: 7 0.207 - 0.259: 7 Chirality restraints: 4746 Sorted by residual: chirality pdb=" CB ILE F 473 " pdb=" CA ILE F 473 " pdb=" CG1 ILE F 473 " pdb=" CG2 ILE F 473 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE C 473 " pdb=" CA ILE C 473 " pdb=" CG1 ILE C 473 " pdb=" CG2 ILE C 473 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE B 473 " pdb=" CA ILE B 473 " pdb=" CG1 ILE B 473 " pdb=" CG2 ILE B 473 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 4743 not shown) Planarity restraints: 5643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 245 " -0.016 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP N 245 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP N 245 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP N 245 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP N 245 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP N 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP N 245 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 245 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 245 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP N 245 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 245 " -0.015 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP A 245 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 245 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 245 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 245 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 245 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 245 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 245 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 245 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 245 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 245 " 0.015 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 245 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 245 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 245 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 245 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 245 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 245 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 245 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 245 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 245 " -0.004 2.00e-02 2.50e+03 ... (remaining 5640 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1698 2.72 - 3.27: 31363 3.27 - 3.81: 49316 3.81 - 4.36: 57425 4.36 - 4.90: 97095 Nonbonded interactions: 236897 Sorted by model distance: nonbonded pdb=" NH1 ARG D 172 " pdb=" O PRO D 173 " model vdw 2.177 3.120 nonbonded pdb=" NH1 ARG A 172 " pdb=" O PRO A 173 " model vdw 2.178 3.120 nonbonded pdb=" NH1 ARG C 172 " pdb=" O PRO C 173 " model vdw 2.178 3.120 nonbonded pdb=" NH1 ARG N 172 " pdb=" O PRO N 173 " model vdw 2.178 3.120 nonbonded pdb=" NH1 ARG B 172 " pdb=" O PRO B 173 " model vdw 2.178 3.120 ... (remaining 236892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 136 through 653 or (resid 654 and (name N or name CA or na \ me C or name O or name CB )) or resid 655 through 716)) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'N' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.530 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.007 0.415 31214 Z= 0.355 Angle : 1.084 64.078 42599 Z= 0.561 Chirality : 0.044 0.259 4746 Planarity : 0.004 0.042 5643 Dihedral : 13.666 85.009 10650 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.13), residues: 3997 helix: -4.08 (0.23), residues: 84 sheet: -0.10 (0.14), residues: 1428 loop : -1.51 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 172 TYR 0.011 0.001 TYR C 241 PHE 0.024 0.002 PHE E 688 TRP 0.051 0.003 TRP N 245 HIS 0.004 0.001 HIS F 419 Details of bonding type rmsd covalent geometry : bond 0.00354 (31207) covalent geometry : angle 0.67814 (42585) SS BOND : bond 0.41263 ( 7) SS BOND : angle 46.62760 ( 14) hydrogen bonds : bond 0.30223 ( 995) hydrogen bonds : angle 10.86308 ( 2544) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6583 (p90) cc_final: 0.6027 (p90) REVERT: A 345 GLN cc_start: 0.5292 (mt0) cc_final: 0.4938 (mt0) REVERT: A 417 TYR cc_start: 0.6075 (t80) cc_final: 0.5325 (t80) REVERT: A 514 ASP cc_start: 0.6307 (t0) cc_final: 0.5635 (t0) REVERT: B 288 PHE cc_start: 0.6603 (p90) cc_final: 0.5979 (p90) REVERT: B 417 TYR cc_start: 0.5872 (t80) cc_final: 0.5288 (t80) REVERT: B 597 MET cc_start: 0.3613 (ttp) cc_final: 0.3216 (mtt) REVERT: C 345 GLN cc_start: 0.5134 (mt0) cc_final: 0.4869 (tt0) REVERT: C 417 TYR cc_start: 0.6120 (t80) cc_final: 0.5304 (t80) REVERT: C 428 PHE cc_start: 0.7357 (m-10) cc_final: 0.6899 (m-80) REVERT: D 214 ASP cc_start: 0.7513 (t0) cc_final: 0.7296 (t0) REVERT: D 318 TRP cc_start: 0.7482 (m-10) cc_final: 0.7088 (m-10) REVERT: D 345 GLN cc_start: 0.5514 (mt0) cc_final: 0.5292 (mt0) REVERT: D 417 TYR cc_start: 0.5915 (t80) cc_final: 0.5243 (t80) REVERT: D 428 PHE cc_start: 0.7283 (m-10) cc_final: 0.7082 (m-80) REVERT: D 699 LEU cc_start: 0.7657 (mm) cc_final: 0.7183 (tt) REVERT: E 214 ASP cc_start: 0.7515 (t0) cc_final: 0.7283 (t0) REVERT: E 318 TRP cc_start: 0.7523 (m-10) cc_final: 0.7015 (m-10) REVERT: E 345 GLN cc_start: 0.5644 (mt0) cc_final: 0.5305 (mt0) REVERT: E 417 TYR cc_start: 0.5920 (t80) cc_final: 0.5304 (t80) REVERT: F 224 ASP cc_start: 0.7303 (m-30) cc_final: 0.7091 (m-30) REVERT: F 318 TRP cc_start: 0.7529 (m-10) cc_final: 0.7224 (m-10) REVERT: F 417 TYR cc_start: 0.6075 (t80) cc_final: 0.5446 (t80) REVERT: F 428 PHE cc_start: 0.7530 (m-10) cc_final: 0.7146 (m-80) REVERT: F 699 LEU cc_start: 0.7468 (mm) cc_final: 0.6932 (tt) REVERT: N 224 ASP cc_start: 0.7477 (m-30) cc_final: 0.7246 (m-30) REVERT: N 345 GLN cc_start: 0.5408 (mt0) cc_final: 0.4940 (mt0) REVERT: N 417 TYR cc_start: 0.6130 (t80) cc_final: 0.5505 (t80) REVERT: N 699 LEU cc_start: 0.7538 (mm) cc_final: 0.7015 (tt) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.1784 time to fit residues: 186.9224 Evaluate side-chains 338 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 161 ASN A 275 ASN A 336 GLN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 582 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 161 ASN B 275 ASN B 336 GLN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 508 ASN B 582 ASN B 698 GLN C 149 ASN C 161 ASN C 275 ASN C 336 GLN C 508 ASN C 582 ASN C 698 GLN D 149 ASN D 161 ASN D 275 ASN D 336 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 ASN D 508 ASN D 698 GLN E 149 ASN E 161 ASN E 275 ASN E 508 ASN E 555 GLN E 582 ASN E 698 GLN F 149 ASN F 161 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN F 336 GLN F 345 GLN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 ASN N 161 ASN N 275 ASN ** N 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 508 ASN ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.189130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154630 restraints weight = 38661.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152882 restraints weight = 68044.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153612 restraints weight = 63418.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153214 restraints weight = 47012.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153522 restraints weight = 44400.624| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 31214 Z= 0.216 Angle : 0.688 11.290 42599 Z= 0.374 Chirality : 0.048 0.245 4746 Planarity : 0.005 0.049 5643 Dihedral : 5.347 18.612 4383 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.22 % Allowed : 12.31 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 3997 helix: -5.19 (0.09), residues: 42 sheet: 0.22 (0.15), residues: 1239 loop : -1.29 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 282 TYR 0.027 0.002 TYR C 184 PHE 0.027 0.002 PHE C 280 TRP 0.031 0.003 TRP E 245 HIS 0.006 0.002 HIS N 221 Details of bonding type rmsd covalent geometry : bond 0.00497 (31207) covalent geometry : angle 0.68779 (42585) SS BOND : bond 0.00207 ( 7) SS BOND : angle 1.47905 ( 14) hydrogen bonds : bond 0.04594 ( 995) hydrogen bonds : angle 6.94803 ( 2544) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 363 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.6881 (m) cc_final: 0.6603 (m) REVERT: A 664 PHE cc_start: 0.6835 (m-80) cc_final: 0.6494 (m-80) REVERT: B 161 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (t0) REVERT: B 346 GLN cc_start: 0.8112 (tp40) cc_final: 0.7804 (tp40) REVERT: B 514 ASP cc_start: 0.7625 (t0) cc_final: 0.7361 (t0) REVERT: C 597 MET cc_start: 0.6205 (mtt) cc_final: 0.4987 (ttt) REVERT: E 211 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7007 (mp) REVERT: E 220 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8821 (pt) REVERT: E 498 ASP cc_start: 0.7699 (p0) cc_final: 0.7426 (p0) REVERT: N 525 ASN cc_start: 0.7719 (p0) cc_final: 0.7457 (p0) REVERT: N 664 PHE cc_start: 0.7058 (m-80) cc_final: 0.6743 (m-80) outliers start: 100 outliers final: 61 residues processed: 432 average time/residue: 0.1671 time to fit residues: 120.2730 Evaluate side-chains 352 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 374 SER Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 273 VAL Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 549 SER Chi-restraints excluded: chain N residue 589 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 310 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 396 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN C 716 ASN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 223 ASN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 161 ASN ** N 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.184350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155752 restraints weight = 37738.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154051 restraints weight = 72048.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153970 restraints weight = 72927.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152767 restraints weight = 55986.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153211 restraints weight = 49969.049| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31214 Z= 0.219 Angle : 0.643 9.624 42599 Z= 0.347 Chirality : 0.046 0.172 4746 Planarity : 0.005 0.049 5643 Dihedral : 5.205 21.694 4383 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.87 % Allowed : 13.54 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 3997 helix: -5.34 (0.09), residues: 42 sheet: -0.10 (0.15), residues: 1316 loop : -1.26 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 330 TYR 0.022 0.002 TYR D 321 PHE 0.028 0.002 PHE A 242 TRP 0.022 0.002 TRP A 245 HIS 0.009 0.002 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00504 (31207) covalent geometry : angle 0.64295 (42585) SS BOND : bond 0.00104 ( 7) SS BOND : angle 0.94559 ( 14) hydrogen bonds : bond 0.04435 ( 995) hydrogen bonds : angle 6.58258 ( 2544) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 343 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8165 (t-100) cc_final: 0.7870 (t-100) REVERT: A 402 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 468 PHE cc_start: 0.8344 (m-80) cc_final: 0.8123 (m-80) REVERT: A 486 CYS cc_start: 0.6722 (m) cc_final: 0.6379 (m) REVERT: A 597 MET cc_start: 0.6297 (mtt) cc_final: 0.4696 (ttt) REVERT: A 664 PHE cc_start: 0.6986 (m-80) cc_final: 0.6784 (m-80) REVERT: B 346 GLN cc_start: 0.8037 (tp40) cc_final: 0.7697 (tp40) REVERT: B 402 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8227 (mt) REVERT: C 323 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8291 (p) REVERT: C 597 MET cc_start: 0.6439 (mtt) cc_final: 0.4840 (ttt) REVERT: D 163 TRP cc_start: 0.8138 (t-100) cc_final: 0.7889 (t-100) REVERT: D 402 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8150 (mt) REVERT: E 163 TRP cc_start: 0.8127 (t-100) cc_final: 0.7875 (t-100) REVERT: E 220 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8737 (pt) REVERT: F 163 TRP cc_start: 0.8097 (t-100) cc_final: 0.7842 (t-100) REVERT: F 402 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8301 (mt) REVERT: F 486 CYS cc_start: 0.7025 (m) cc_final: 0.6766 (m) REVERT: N 163 TRP cc_start: 0.8217 (t-100) cc_final: 0.7971 (t-100) REVERT: N 253 ASP cc_start: 0.7607 (p0) cc_final: 0.7404 (p0) REVERT: N 288 PHE cc_start: 0.8010 (p90) cc_final: 0.7585 (p90) REVERT: N 402 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8038 (mp) REVERT: N 486 CYS cc_start: 0.6828 (m) cc_final: 0.6601 (m) REVERT: N 597 MET cc_start: 0.5257 (mtt) cc_final: 0.4455 (ttt) outliers start: 151 outliers final: 90 residues processed: 443 average time/residue: 0.1527 time to fit residues: 114.4438 Evaluate side-chains 391 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 294 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 552 HIS Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain N residue 196 ILE Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 275 ASN Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 366 optimal weight: 0.7980 chunk 349 optimal weight: 1.9990 chunk 110 optimal weight: 50.0000 chunk 290 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 318 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 95 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 427 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 427 GLN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 427 GLN F 474 GLN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.185311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155712 restraints weight = 37854.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153907 restraints weight = 60218.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149789 restraints weight = 67879.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148539 restraints weight = 75735.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.149067 restraints weight = 64878.923| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31214 Z= 0.149 Angle : 0.565 8.762 42599 Z= 0.303 Chirality : 0.044 0.153 4746 Planarity : 0.004 0.048 5643 Dihedral : 4.876 20.984 4383 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.71 % Allowed : 16.05 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3997 helix: -5.36 (0.09), residues: 42 sheet: 0.03 (0.15), residues: 1302 loop : -1.25 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 330 TYR 0.017 0.001 TYR E 562 PHE 0.017 0.002 PHE A 242 TRP 0.016 0.001 TRP A 245 HIS 0.007 0.001 HIS E 419 Details of bonding type rmsd covalent geometry : bond 0.00345 (31207) covalent geometry : angle 0.56509 (42585) SS BOND : bond 0.00019 ( 7) SS BOND : angle 0.50903 ( 14) hydrogen bonds : bond 0.03463 ( 995) hydrogen bonds : angle 6.08711 ( 2544) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 329 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.6640 (m) cc_final: 0.6378 (m) REVERT: B 346 GLN cc_start: 0.8004 (tp40) cc_final: 0.7664 (tp40) REVERT: B 403 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (mt) REVERT: C 163 TRP cc_start: 0.8018 (t-100) cc_final: 0.7756 (t-100) REVERT: C 243 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7681 (mmm-85) REVERT: C 323 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8331 (p) REVERT: C 597 MET cc_start: 0.6274 (mtt) cc_final: 0.5970 (mtt) REVERT: D 253 ASP cc_start: 0.7473 (p0) cc_final: 0.7246 (p0) REVERT: D 465 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8317 (mp) REVERT: E 163 TRP cc_start: 0.8094 (t-100) cc_final: 0.7840 (t-100) REVERT: E 220 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8729 (pt) REVERT: F 163 TRP cc_start: 0.8066 (t-100) cc_final: 0.7805 (t-100) REVERT: F 323 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8465 (p) REVERT: F 486 CYS cc_start: 0.6954 (m) cc_final: 0.6708 (m) REVERT: N 163 TRP cc_start: 0.8196 (t-100) cc_final: 0.7882 (t-100) REVERT: N 253 ASP cc_start: 0.7585 (p0) cc_final: 0.7352 (p0) REVERT: N 288 PHE cc_start: 0.8025 (p90) cc_final: 0.7553 (p90) outliers start: 115 outliers final: 86 residues processed: 404 average time/residue: 0.1508 time to fit residues: 104.3373 Evaluate side-chains 378 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 287 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 552 HIS Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 398 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 649 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 217 optimal weight: 40.0000 chunk 180 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 282 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 296 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 GLN B 364 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 GLN ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 GLN N 161 ASN ** N 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 698 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.164435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121727 restraints weight = 40186.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119200 restraints weight = 55272.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120357 restraints weight = 55154.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120552 restraints weight = 38478.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120952 restraints weight = 35971.708| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.065 31214 Z= 0.431 Angle : 0.846 8.566 42599 Z= 0.462 Chirality : 0.052 0.241 4746 Planarity : 0.006 0.054 5643 Dihedral : 6.078 27.441 4383 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 7.22 % Allowed : 15.70 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.13), residues: 3997 helix: -5.46 (0.09), residues: 42 sheet: -0.71 (0.14), residues: 1456 loop : -1.62 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 330 TYR 0.036 0.003 TYR A 321 PHE 0.035 0.003 PHE N 231 TRP 0.037 0.003 TRP N 245 HIS 0.020 0.003 HIS N 221 Details of bonding type rmsd covalent geometry : bond 0.00994 (31207) covalent geometry : angle 0.84639 (42585) SS BOND : bond 0.00080 ( 7) SS BOND : angle 0.87533 ( 14) hydrogen bonds : bond 0.05372 ( 995) hydrogen bonds : angle 7.06818 ( 2544) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 360 time to evaluate : 1.192 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 163 TRP cc_start: 0.8680 (t-100) cc_final: 0.8211 (t-100) REVERT: A 185 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8001 (ttp80) REVERT: A 253 ASP cc_start: 0.7710 (p0) cc_final: 0.7489 (p0) REVERT: A 288 PHE cc_start: 0.8298 (p90) cc_final: 0.7969 (p90) REVERT: A 428 PHE cc_start: 0.7701 (m-10) cc_final: 0.7366 (m-80) REVERT: A 597 MET cc_start: 0.6396 (mtt) cc_final: 0.6166 (mtt) REVERT: B 231 PHE cc_start: 0.7307 (m-80) cc_final: 0.6858 (m-80) REVERT: B 253 ASP cc_start: 0.7828 (p0) cc_final: 0.7522 (p0) REVERT: B 261 SER cc_start: 0.7874 (p) cc_final: 0.7578 (m) REVERT: B 323 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 402 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 417 TYR cc_start: 0.6843 (t80) cc_final: 0.6351 (t80) REVERT: B 664 PHE cc_start: 0.7420 (m-80) cc_final: 0.7097 (m-80) REVERT: C 158 THR cc_start: 0.9112 (m) cc_final: 0.8765 (t) REVERT: C 163 TRP cc_start: 0.8631 (t-100) cc_final: 0.8155 (t-100) REVERT: C 185 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8234 (ttp80) REVERT: C 211 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7249 (mp) REVERT: C 243 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7615 (mmm-85) REVERT: C 253 ASP cc_start: 0.7838 (p0) cc_final: 0.7550 (p0) REVERT: C 323 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (p) REVERT: C 428 PHE cc_start: 0.7717 (m-10) cc_final: 0.7219 (m-80) REVERT: C 559 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7007 (pt) REVERT: D 163 TRP cc_start: 0.8649 (t-100) cc_final: 0.8030 (t-100) REVERT: D 185 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8218 (ttp80) REVERT: D 243 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.8103 (tpp80) REVERT: D 253 ASP cc_start: 0.7860 (p0) cc_final: 0.7643 (p0) REVERT: D 402 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8076 (mt) REVERT: D 417 TYR cc_start: 0.6684 (t80) cc_final: 0.6330 (t80) REVERT: D 664 PHE cc_start: 0.7649 (m-80) cc_final: 0.7326 (m-80) REVERT: E 163 TRP cc_start: 0.8690 (t-100) cc_final: 0.8150 (t-100) REVERT: E 185 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8210 (ttt-90) REVERT: E 220 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8911 (pt) REVERT: E 417 TYR cc_start: 0.6972 (t80) cc_final: 0.6645 (t80) REVERT: E 428 PHE cc_start: 0.7723 (m-80) cc_final: 0.7335 (m-80) REVERT: E 645 ILE cc_start: 0.8394 (mp) cc_final: 0.8171 (mp) REVERT: E 664 PHE cc_start: 0.7534 (m-80) cc_final: 0.7136 (m-80) REVERT: F 163 TRP cc_start: 0.8656 (t-100) cc_final: 0.8334 (t-100) REVERT: F 185 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8260 (ttp80) REVERT: F 253 ASP cc_start: 0.7803 (p0) cc_final: 0.7596 (p0) REVERT: F 261 SER cc_start: 0.7648 (p) cc_final: 0.7446 (m) REVERT: F 288 PHE cc_start: 0.8503 (p90) cc_final: 0.8177 (p90) REVERT: F 323 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.7889 (m) REVERT: F 402 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8447 (mt) REVERT: F 428 PHE cc_start: 0.7714 (m-10) cc_final: 0.7453 (m-80) REVERT: F 664 PHE cc_start: 0.7629 (m-80) cc_final: 0.7283 (m-80) REVERT: N 158 THR cc_start: 0.9110 (m) cc_final: 0.8904 (t) REVERT: N 163 TRP cc_start: 0.8709 (t-100) cc_final: 0.8259 (t-100) REVERT: N 185 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8199 (ttp80) REVERT: N 253 ASP cc_start: 0.7953 (p0) cc_final: 0.7592 (p0) REVERT: N 288 PHE cc_start: 0.8271 (p90) cc_final: 0.7826 (p90) REVERT: N 402 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8175 (mt) REVERT: N 417 TYR cc_start: 0.6931 (t80) cc_final: 0.6617 (t80) outliers start: 224 outliers final: 157 residues processed: 526 average time/residue: 0.1728 time to fit residues: 148.3976 Evaluate side-chains 468 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 295 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 275 ASN Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain C residue 185 ARG Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 552 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 516 GLU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 600 GLN Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 196 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain N residue 185 ARG Chi-restraints excluded: chain N residue 196 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 275 ASN Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 445 SER Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 549 SER Chi-restraints excluded: chain N residue 559 LEU Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 590 LEU Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 649 SER Chi-restraints excluded: chain N residue 712 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 188 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 304 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 chunk 160 optimal weight: 40.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN C 600 GLN D 161 ASN ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 594 GLN F 600 GLN N 161 ASN N 223 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.174108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130946 restraints weight = 39340.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.128053 restraints weight = 59818.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.129817 restraints weight = 51671.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130323 restraints weight = 34528.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.130617 restraints weight = 32106.197| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31214 Z= 0.115 Angle : 0.575 8.600 42599 Z= 0.305 Chirality : 0.044 0.233 4746 Planarity : 0.004 0.050 5643 Dihedral : 5.010 20.482 4383 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.38 % Allowed : 20.99 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3997 helix: -5.41 (0.09), residues: 42 sheet: -0.13 (0.15), residues: 1281 loop : -1.29 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.020 0.001 TYR E 562 PHE 0.021 0.001 PHE N 231 TRP 0.026 0.001 TRP E 706 HIS 0.006 0.001 HIS D 552 Details of bonding type rmsd covalent geometry : bond 0.00259 (31207) covalent geometry : angle 0.57502 (42585) SS BOND : bond 0.01103 ( 7) SS BOND : angle 0.47223 ( 14) hydrogen bonds : bond 0.03228 ( 995) hydrogen bonds : angle 6.10373 ( 2544) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 357 time to evaluate : 1.085 Fit side-chains REVERT: A 158 THR cc_start: 0.9124 (m) cc_final: 0.8889 (t) REVERT: A 288 PHE cc_start: 0.8213 (p90) cc_final: 0.7936 (p90) REVERT: A 428 PHE cc_start: 0.7631 (m-10) cc_final: 0.7427 (m-10) REVERT: A 597 MET cc_start: 0.6442 (mtt) cc_final: 0.6124 (mtt) REVERT: B 158 THR cc_start: 0.9144 (m) cc_final: 0.8919 (t) REVERT: B 163 TRP cc_start: 0.8417 (t-100) cc_final: 0.8183 (t-100) REVERT: B 231 PHE cc_start: 0.6991 (m-80) cc_final: 0.6790 (m-80) REVERT: B 243 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7787 (mmm-85) REVERT: B 346 GLN cc_start: 0.8152 (tp40) cc_final: 0.7691 (tp40) REVERT: B 417 TYR cc_start: 0.6584 (t80) cc_final: 0.6124 (t80) REVERT: B 664 PHE cc_start: 0.7289 (m-80) cc_final: 0.6943 (m-80) REVERT: C 158 THR cc_start: 0.9017 (m) cc_final: 0.8748 (t) REVERT: C 163 TRP cc_start: 0.8259 (t-100) cc_final: 0.7835 (t-100) REVERT: C 243 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7916 (mmm-85) REVERT: C 428 PHE cc_start: 0.7602 (m-10) cc_final: 0.7253 (m-80) REVERT: C 597 MET cc_start: 0.6875 (mtt) cc_final: 0.6675 (mtt) REVERT: D 158 THR cc_start: 0.9091 (m) cc_final: 0.8863 (t) REVERT: D 161 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7984 (t0) REVERT: D 253 ASP cc_start: 0.7671 (p0) cc_final: 0.7401 (p0) REVERT: D 417 TYR cc_start: 0.6620 (t80) cc_final: 0.6352 (t80) REVERT: D 700 LYS cc_start: 0.8206 (mttt) cc_final: 0.7820 (mttp) REVERT: E 158 THR cc_start: 0.9123 (m) cc_final: 0.8825 (t) REVERT: E 163 TRP cc_start: 0.8372 (t-100) cc_final: 0.7863 (t-100) REVERT: E 220 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8522 (pt) REVERT: E 243 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7983 (ttm-80) REVERT: E 428 PHE cc_start: 0.7591 (m-80) cc_final: 0.7345 (m-80) REVERT: F 158 THR cc_start: 0.9045 (m) cc_final: 0.8716 (p) REVERT: F 163 TRP cc_start: 0.8315 (t-100) cc_final: 0.7914 (t-100) REVERT: F 220 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8634 (pt) REVERT: F 253 ASP cc_start: 0.7676 (p0) cc_final: 0.7419 (p0) REVERT: F 323 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8464 (p) REVERT: F 402 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8360 (mt) REVERT: F 407 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8693 (m) REVERT: F 428 PHE cc_start: 0.7513 (m-10) cc_final: 0.7249 (m-80) REVERT: F 664 PHE cc_start: 0.7543 (m-80) cc_final: 0.7140 (m-80) REVERT: N 158 THR cc_start: 0.9048 (m) cc_final: 0.8684 (p) REVERT: N 163 TRP cc_start: 0.8387 (t-100) cc_final: 0.7944 (t-100) REVERT: N 220 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8698 (pt) REVERT: N 253 ASP cc_start: 0.7697 (p0) cc_final: 0.7406 (p0) REVERT: N 288 PHE cc_start: 0.8146 (p90) cc_final: 0.7675 (p90) REVERT: N 323 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8396 (p) REVERT: N 402 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8026 (mt) REVERT: N 417 TYR cc_start: 0.6525 (t80) cc_final: 0.6310 (t80) REVERT: N 428 PHE cc_start: 0.7708 (m-10) cc_final: 0.7498 (m-80) outliers start: 105 outliers final: 70 residues processed: 427 average time/residue: 0.1675 time to fit residues: 120.8019 Evaluate side-chains 394 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 314 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 364 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 533 GLU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 215 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 273 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 367 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.168220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125016 restraints weight = 40052.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121826 restraints weight = 60675.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124002 restraints weight = 56418.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123801 restraints weight = 37044.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124987 restraints weight = 34678.195| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 31214 Z= 0.248 Angle : 0.673 8.840 42599 Z= 0.359 Chirality : 0.046 0.209 4746 Planarity : 0.005 0.050 5643 Dihedral : 5.262 21.717 4383 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.61 % Allowed : 20.47 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 3997 helix: -5.43 (0.09), residues: 42 sheet: -0.34 (0.14), residues: 1414 loop : -1.55 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 330 TYR 0.024 0.002 TYR F 321 PHE 0.029 0.002 PHE N 231 TRP 0.018 0.002 TRP N 245 HIS 0.010 0.002 HIS N 221 Details of bonding type rmsd covalent geometry : bond 0.00572 (31207) covalent geometry : angle 0.67312 (42585) SS BOND : bond 0.00139 ( 7) SS BOND : angle 1.18167 ( 14) hydrogen bonds : bond 0.04100 ( 995) hydrogen bonds : angle 6.32025 ( 2544) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 334 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8587 (t-100) cc_final: 0.8022 (t-100) REVERT: A 185 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8033 (ttp80) REVERT: A 283 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8664 (ptpt) REVERT: A 288 PHE cc_start: 0.8239 (p90) cc_final: 0.7904 (p90) REVERT: A 428 PHE cc_start: 0.7660 (m-10) cc_final: 0.7335 (m-80) REVERT: A 464 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: A 597 MET cc_start: 0.6562 (mtt) cc_final: 0.6271 (mtt) REVERT: A 700 LYS cc_start: 0.7694 (mmtm) cc_final: 0.6932 (mttm) REVERT: B 172 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7166 (ptm160) REVERT: B 231 PHE cc_start: 0.7211 (m-80) cc_final: 0.6830 (m-80) REVERT: B 243 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7983 (mmm-85) REVERT: B 323 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 402 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 464 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: B 664 PHE cc_start: 0.7493 (m-80) cc_final: 0.7159 (m-80) REVERT: C 163 TRP cc_start: 0.8526 (t-100) cc_final: 0.8023 (t-100) REVERT: C 243 ARG cc_start: 0.8273 (tpp80) cc_final: 0.8049 (mmm-85) REVERT: C 253 ASP cc_start: 0.7693 (p0) cc_final: 0.7372 (p0) REVERT: C 323 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 428 PHE cc_start: 0.7650 (m-10) cc_final: 0.7194 (m-80) REVERT: D 163 TRP cc_start: 0.8500 (t-100) cc_final: 0.7869 (t-100) REVERT: D 185 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8198 (ttp80) REVERT: D 253 ASP cc_start: 0.7759 (p0) cc_final: 0.7473 (p0) REVERT: D 346 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: D 402 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8151 (mt) REVERT: D 417 TYR cc_start: 0.6774 (t80) cc_final: 0.6343 (t80) REVERT: D 664 PHE cc_start: 0.7392 (m-80) cc_final: 0.7020 (m-80) REVERT: D 700 LYS cc_start: 0.8289 (mttt) cc_final: 0.7961 (mttp) REVERT: E 158 THR cc_start: 0.9183 (m) cc_final: 0.8942 (t) REVERT: E 163 TRP cc_start: 0.8597 (t-100) cc_final: 0.8025 (t-100) REVERT: E 185 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8241 (ttp80) REVERT: E 220 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8839 (pt) REVERT: E 428 PHE cc_start: 0.7670 (m-80) cc_final: 0.7370 (m-80) REVERT: E 546 SER cc_start: 0.7947 (m) cc_final: 0.7397 (t) REVERT: E 664 PHE cc_start: 0.7581 (m-80) cc_final: 0.7151 (m-80) REVERT: F 163 TRP cc_start: 0.8559 (t-100) cc_final: 0.8074 (t-100) REVERT: F 185 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: F 253 ASP cc_start: 0.7880 (p0) cc_final: 0.7646 (p0) REVERT: F 283 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8505 (ptpt) REVERT: F 323 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.7642 (m) REVERT: F 402 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8423 (mt) REVERT: F 428 PHE cc_start: 0.7692 (m-10) cc_final: 0.7366 (m-80) REVERT: F 664 PHE cc_start: 0.7667 (m-80) cc_final: 0.7308 (m-80) REVERT: F 715 LEU cc_start: 0.7250 (mt) cc_final: 0.6702 (tp) REVERT: N 158 THR cc_start: 0.9055 (m) cc_final: 0.8818 (p) REVERT: N 163 TRP cc_start: 0.8567 (t-100) cc_final: 0.8081 (t-100) REVERT: N 185 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (ttp80) REVERT: N 253 ASP cc_start: 0.7790 (p0) cc_final: 0.7496 (p0) REVERT: N 288 PHE cc_start: 0.8196 (p90) cc_final: 0.7727 (p90) REVERT: N 402 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8088 (mt) REVERT: N 417 TYR cc_start: 0.6726 (t80) cc_final: 0.6413 (t80) outliers start: 174 outliers final: 132 residues processed: 450 average time/residue: 0.1791 time to fit residues: 132.8769 Evaluate side-chains 460 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 309 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain N residue 185 ARG Chi-restraints excluded: chain N residue 196 ILE Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 533 GLU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 549 SER Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 649 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 216 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 193 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 252 optimal weight: 3.9990 chunk 275 optimal weight: 20.0000 chunk 187 optimal weight: 40.0000 chunk 304 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN E 698 GLN E 712 GLN N 698 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125069 restraints weight = 39895.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122416 restraints weight = 57143.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124419 restraints weight = 54722.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124314 restraints weight = 36515.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125373 restraints weight = 33672.754| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31214 Z= 0.229 Angle : 0.659 8.624 42599 Z= 0.350 Chirality : 0.046 0.200 4746 Planarity : 0.004 0.050 5643 Dihedral : 5.240 22.365 4383 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.64 % Allowed : 21.31 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3997 helix: -5.42 (0.09), residues: 42 sheet: -0.36 (0.14), residues: 1414 loop : -1.62 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 572 TYR 0.021 0.002 TYR F 321 PHE 0.026 0.002 PHE N 231 TRP 0.018 0.002 TRP E 245 HIS 0.010 0.002 HIS B 419 Details of bonding type rmsd covalent geometry : bond 0.00531 (31207) covalent geometry : angle 0.65864 (42585) SS BOND : bond 0.00410 ( 7) SS BOND : angle 1.03746 ( 14) hydrogen bonds : bond 0.03933 ( 995) hydrogen bonds : angle 6.21661 ( 2544) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 331 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8583 (t-100) cc_final: 0.8019 (t-100) REVERT: A 288 PHE cc_start: 0.8239 (p90) cc_final: 0.7898 (p90) REVERT: A 428 PHE cc_start: 0.7627 (m-10) cc_final: 0.7300 (m-80) REVERT: A 464 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: A 597 MET cc_start: 0.6552 (mtt) cc_final: 0.6336 (mtt) REVERT: A 664 PHE cc_start: 0.7408 (m-80) cc_final: 0.7093 (m-80) REVERT: A 700 LYS cc_start: 0.7804 (mmtm) cc_final: 0.7027 (mttm) REVERT: A 715 LEU cc_start: 0.7116 (mt) cc_final: 0.6526 (tp) REVERT: B 231 PHE cc_start: 0.7285 (m-80) cc_final: 0.6965 (m-80) REVERT: B 323 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8400 (p) REVERT: B 346 GLN cc_start: 0.8142 (tp40) cc_final: 0.7603 (tp40) REVERT: B 402 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 464 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: B 664 PHE cc_start: 0.7561 (m-80) cc_final: 0.7247 (m-80) REVERT: C 163 TRP cc_start: 0.8498 (t-100) cc_final: 0.7963 (t-100) REVERT: C 243 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7881 (mmm-85) REVERT: C 253 ASP cc_start: 0.7716 (p0) cc_final: 0.7401 (p0) REVERT: C 323 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 419 HIS cc_start: 0.5805 (OUTLIER) cc_final: 0.4579 (m90) REVERT: C 597 MET cc_start: 0.6531 (mtt) cc_final: 0.6319 (mmt) REVERT: D 163 TRP cc_start: 0.8492 (t-100) cc_final: 0.7952 (t-100) REVERT: D 185 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8308 (ttp80) REVERT: D 243 ARG cc_start: 0.8431 (tpp-160) cc_final: 0.8210 (tpp80) REVERT: D 253 ASP cc_start: 0.7722 (p0) cc_final: 0.7439 (p0) REVERT: D 402 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8147 (mt) REVERT: E 158 THR cc_start: 0.9160 (m) cc_final: 0.8955 (t) REVERT: E 163 TRP cc_start: 0.8529 (t-100) cc_final: 0.7996 (t-100) REVERT: E 185 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8166 (ttp80) REVERT: E 220 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8821 (pt) REVERT: E 546 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7359 (t) REVERT: E 664 PHE cc_start: 0.7650 (m-80) cc_final: 0.7263 (m-80) REVERT: F 163 TRP cc_start: 0.8499 (t-100) cc_final: 0.8024 (t-100) REVERT: F 185 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (ttp80) REVERT: F 253 ASP cc_start: 0.7790 (p0) cc_final: 0.7561 (p0) REVERT: F 323 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8438 (p) REVERT: F 402 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8387 (mt) REVERT: F 428 PHE cc_start: 0.7638 (m-10) cc_final: 0.7341 (m-80) REVERT: F 664 PHE cc_start: 0.7640 (m-80) cc_final: 0.7309 (m-80) REVERT: F 715 LEU cc_start: 0.7142 (mt) cc_final: 0.6716 (tp) REVERT: N 158 THR cc_start: 0.9064 (m) cc_final: 0.8831 (p) REVERT: N 163 TRP cc_start: 0.8523 (t-100) cc_final: 0.7982 (t-100) REVERT: N 185 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8206 (ttp80) REVERT: N 220 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8841 (pt) REVERT: N 253 ASP cc_start: 0.7790 (p0) cc_final: 0.7494 (p0) REVERT: N 288 PHE cc_start: 0.8189 (p90) cc_final: 0.7751 (p90) REVERT: N 402 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8122 (mt) REVERT: N 417 TYR cc_start: 0.6820 (t80) cc_final: 0.6511 (t80) outliers start: 175 outliers final: 140 residues processed: 442 average time/residue: 0.1619 time to fit residues: 121.2098 Evaluate side-chains 466 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 309 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 419 HIS Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain N residue 185 ARG Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 434 ASP Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 533 GLU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 543 ASN Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 549 SER Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 373 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 698 GLN ** N 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 555 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 = 0.3980 r_free = 0.3980 target = 0.167225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123099 restraints weight = 39995.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120100 restraints weight = 60596.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121833 restraints weight = 55063.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122631 restraints weight = 36672.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.123089 restraints weight = 33096.231| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 31214 Z= 0.234 Angle : 0.675 8.770 42599 Z= 0.358 Chirality : 0.046 0.201 4746 Planarity : 0.005 0.049 5643 Dihedral : 5.265 22.033 4383 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.93 % Allowed : 22.31 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3997 helix: -5.42 (0.09), residues: 42 sheet: -0.38 (0.14), residues: 1414 loop : -1.68 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 330 TYR 0.022 0.002 TYR A 321 PHE 0.027 0.002 PHE N 231 TRP 0.015 0.002 TRP N 245 HIS 0.009 0.002 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00543 (31207) covalent geometry : angle 0.67475 (42585) SS BOND : bond 0.00253 ( 7) SS BOND : angle 1.21978 ( 14) hydrogen bonds : bond 0.03981 ( 995) hydrogen bonds : angle 6.20562 ( 2544) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 323 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8610 (t-100) cc_final: 0.8005 (t-100) REVERT: A 185 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8066 (ttt-90) REVERT: A 283 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8619 (ptpt) REVERT: A 288 PHE cc_start: 0.8241 (p90) cc_final: 0.7884 (p90) REVERT: A 428 PHE cc_start: 0.7566 (m-10) cc_final: 0.7111 (m-80) REVERT: A 464 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7102 (mt0) REVERT: A 597 MET cc_start: 0.6743 (mtt) cc_final: 0.6495 (mtt) REVERT: A 664 PHE cc_start: 0.7422 (m-80) cc_final: 0.7131 (m-80) REVERT: A 700 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7036 (mttm) REVERT: A 715 LEU cc_start: 0.7205 (mt) cc_final: 0.6721 (tp) REVERT: B 231 PHE cc_start: 0.7430 (m-80) cc_final: 0.6989 (m-80) REVERT: B 243 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7061 (mpt-90) REVERT: B 323 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 402 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8285 (mt) REVERT: B 464 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: B 546 SER cc_start: 0.8188 (m) cc_final: 0.7548 (t) REVERT: B 664 PHE cc_start: 0.7683 (m-80) cc_final: 0.7359 (m-80) REVERT: C 163 TRP cc_start: 0.8527 (t-100) cc_final: 0.7969 (t-100) REVERT: C 243 ARG cc_start: 0.8312 (tpp80) cc_final: 0.7922 (mmm-85) REVERT: C 253 ASP cc_start: 0.7801 (p0) cc_final: 0.7495 (p0) REVERT: C 323 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 428 PHE cc_start: 0.7583 (m-10) cc_final: 0.7212 (m-80) REVERT: C 559 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7159 (pt) REVERT: C 715 LEU cc_start: 0.7359 (mt) cc_final: 0.6825 (tp) REVERT: D 163 TRP cc_start: 0.8545 (t-100) cc_final: 0.7900 (t-100) REVERT: D 185 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8089 (ttp80) REVERT: D 243 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8257 (tpp80) REVERT: D 253 ASP cc_start: 0.7810 (p0) cc_final: 0.7518 (p0) REVERT: D 315 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: D 346 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8123 (tp40) REVERT: D 402 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8139 (mt) REVERT: E 163 TRP cc_start: 0.8625 (t-100) cc_final: 0.8054 (t-100) REVERT: E 185 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8063 (ttp80) REVERT: E 220 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8817 (pt) REVERT: E 323 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8360 (p) REVERT: E 428 PHE cc_start: 0.7704 (m-80) cc_final: 0.7344 (m-80) REVERT: E 546 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7421 (t) REVERT: E 664 PHE cc_start: 0.7682 (m-80) cc_final: 0.7323 (m-80) REVERT: E 715 LEU cc_start: 0.7405 (mt) cc_final: 0.6762 (tp) REVERT: F 163 TRP cc_start: 0.8576 (t-100) cc_final: 0.8070 (t-100) REVERT: F 185 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8285 (ttp80) REVERT: F 253 ASP cc_start: 0.7821 (p0) cc_final: 0.7598 (p0) REVERT: F 283 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8726 (ptpt) REVERT: F 288 PHE cc_start: 0.8386 (p90) cc_final: 0.8040 (p90) REVERT: F 323 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8377 (p) REVERT: F 402 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8397 (mt) REVERT: F 428 PHE cc_start: 0.7667 (m-10) cc_final: 0.7331 (m-80) REVERT: F 664 PHE cc_start: 0.7675 (m-80) cc_final: 0.7364 (m-80) REVERT: F 715 LEU cc_start: 0.7551 (mt) cc_final: 0.7084 (tp) REVERT: N 158 THR cc_start: 0.9030 (m) cc_final: 0.8776 (p) REVERT: N 163 TRP cc_start: 0.8592 (t-100) cc_final: 0.7982 (t-100) REVERT: N 185 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8231 (ttp80) REVERT: N 253 ASP cc_start: 0.7849 (p0) cc_final: 0.7587 (p0) REVERT: N 288 PHE cc_start: 0.8186 (p90) cc_final: 0.7738 (p90) REVERT: N 323 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8252 (p) REVERT: N 402 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8125 (mt) REVERT: N 417 TYR cc_start: 0.6955 (t80) cc_final: 0.6494 (t80) REVERT: N 715 LEU cc_start: 0.7412 (mt) cc_final: 0.6904 (tp) outliers start: 184 outliers final: 147 residues processed: 442 average time/residue: 0.1631 time to fit residues: 121.6230 Evaluate side-chains 473 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 302 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain N residue 185 ARG Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 434 ASP Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 533 GLU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 699 LEU Chi-restraints excluded: chain N residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 275 optimal weight: 30.0000 chunk 183 optimal weight: 0.1980 chunk 186 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 130 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 395 optimal weight: 40.0000 chunk 237 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 31 optimal weight: 0.0020 overall best weight: 2.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 GLN ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124945 restraints weight = 39602.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122263 restraints weight = 57841.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123807 restraints weight = 53731.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124114 restraints weight = 37344.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.124468 restraints weight = 34644.574| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31214 Z= 0.210 Angle : 0.651 8.846 42599 Z= 0.345 Chirality : 0.046 0.184 4746 Planarity : 0.004 0.050 5643 Dihedral : 5.152 22.245 4383 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.74 % Allowed : 22.63 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.13), residues: 3997 helix: -5.42 (0.09), residues: 42 sheet: -0.29 (0.14), residues: 1414 loop : -1.67 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 372 TYR 0.020 0.002 TYR F 321 PHE 0.026 0.002 PHE N 231 TRP 0.016 0.002 TRP N 245 HIS 0.008 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00490 (31207) covalent geometry : angle 0.65077 (42585) SS BOND : bond 0.00167 ( 7) SS BOND : angle 1.14455 ( 14) hydrogen bonds : bond 0.03797 ( 995) hydrogen bonds : angle 6.06865 ( 2544) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7994 Ramachandran restraints generated. 3997 Oldfield, 0 Emsley, 3997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 320 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TRP cc_start: 0.8567 (t-100) cc_final: 0.8017 (t-100) REVERT: A 185 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7989 (ttt-90) REVERT: A 283 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8663 (ptpt) REVERT: A 288 PHE cc_start: 0.8215 (p90) cc_final: 0.7869 (p90) REVERT: A 419 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.4556 (m90) REVERT: A 464 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: A 664 PHE cc_start: 0.7422 (m-80) cc_final: 0.7132 (m-80) REVERT: A 700 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7039 (mttm) REVERT: A 715 LEU cc_start: 0.7059 (mt) cc_final: 0.6624 (tp) REVERT: B 231 PHE cc_start: 0.7449 (m-80) cc_final: 0.7011 (m-80) REVERT: B 243 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7111 (mpt-90) REVERT: B 323 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8414 (p) REVERT: B 346 GLN cc_start: 0.8174 (tp40) cc_final: 0.7593 (tp40) REVERT: B 402 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 464 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: B 546 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7361 (t) REVERT: B 664 PHE cc_start: 0.7759 (m-80) cc_final: 0.7491 (m-80) REVERT: B 715 LEU cc_start: 0.7190 (mt) cc_final: 0.6913 (tp) REVERT: C 163 TRP cc_start: 0.8455 (t-100) cc_final: 0.7907 (t-100) REVERT: C 243 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7908 (mmm-85) REVERT: C 323 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 419 HIS cc_start: 0.5822 (OUTLIER) cc_final: 0.4514 (m90) REVERT: C 559 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7210 (pt) REVERT: C 715 LEU cc_start: 0.7256 (mt) cc_final: 0.6842 (tp) REVERT: D 163 TRP cc_start: 0.8489 (t-100) cc_final: 0.7860 (t-100) REVERT: D 185 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8253 (ttp80) REVERT: D 243 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8245 (tpp80) REVERT: D 253 ASP cc_start: 0.7810 (p0) cc_final: 0.7511 (p0) REVERT: D 315 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: D 346 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (tp40) REVERT: D 402 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8143 (mt) REVERT: D 715 LEU cc_start: 0.7265 (mt) cc_final: 0.6798 (tp) REVERT: E 163 TRP cc_start: 0.8599 (t-100) cc_final: 0.8018 (t-100) REVERT: E 185 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8224 (ttp80) REVERT: E 220 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8769 (pt) REVERT: E 323 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8393 (p) REVERT: E 428 PHE cc_start: 0.7688 (m-80) cc_final: 0.7315 (m-80) REVERT: E 546 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7371 (t) REVERT: E 664 PHE cc_start: 0.7675 (m-80) cc_final: 0.7315 (m-80) REVERT: E 715 LEU cc_start: 0.7434 (mt) cc_final: 0.6958 (tp) REVERT: F 163 TRP cc_start: 0.8549 (t-100) cc_final: 0.8045 (t-100) REVERT: F 185 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8248 (ttp80) REVERT: F 253 ASP cc_start: 0.7750 (p0) cc_final: 0.7516 (p0) REVERT: F 283 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8765 (ptpt) REVERT: F 288 PHE cc_start: 0.8363 (p90) cc_final: 0.8034 (p90) REVERT: F 323 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8379 (p) REVERT: F 402 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8434 (mt) REVERT: F 428 PHE cc_start: 0.7663 (m-10) cc_final: 0.7423 (m-80) REVERT: F 664 PHE cc_start: 0.7642 (m-80) cc_final: 0.7352 (m-80) REVERT: F 715 LEU cc_start: 0.7572 (mt) cc_final: 0.7174 (tp) REVERT: N 158 THR cc_start: 0.9031 (m) cc_final: 0.8777 (p) REVERT: N 163 TRP cc_start: 0.8550 (t-100) cc_final: 0.7949 (t-100) REVERT: N 185 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8108 (ttp80) REVERT: N 220 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8877 (pt) REVERT: N 253 ASP cc_start: 0.7853 (p0) cc_final: 0.7577 (p0) REVERT: N 288 PHE cc_start: 0.8164 (p90) cc_final: 0.7731 (p90) REVERT: N 323 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8199 (p) REVERT: N 356 ARG cc_start: 0.8291 (mtp180) cc_final: 0.8004 (mtp180) REVERT: N 402 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8113 (mt) REVERT: N 417 TYR cc_start: 0.6942 (t80) cc_final: 0.6544 (t80) REVERT: N 715 LEU cc_start: 0.7401 (mt) cc_final: 0.6985 (tp) outliers start: 178 outliers final: 147 residues processed: 432 average time/residue: 0.1608 time to fit residues: 117.1870 Evaluate side-chains 480 residues out of total 3367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 305 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 283 LYS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 464 GLN Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 419 HIS Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 312 SER Chi-restraints excluded: chain D residue 315 GLN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 441 THR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 533 GLU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 711 VAL Chi-restraints excluded: chain E residue 185 ARG Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 374 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 508 ASN Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 543 ASN Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain E residue 593 THR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 185 ARG Chi-restraints excluded: chain F residue 193 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 283 LYS Chi-restraints excluded: chain F residue 293 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 434 ASP Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 441 THR Chi-restraints excluded: chain F residue 508 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 549 SER Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain N residue 185 ARG Chi-restraints excluded: chain N residue 211 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 292 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 312 SER Chi-restraints excluded: chain N residue 323 THR Chi-restraints excluded: chain N residue 328 ILE Chi-restraints excluded: chain N residue 365 THR Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 385 MET Chi-restraints excluded: chain N residue 398 SER Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 403 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 434 ASP Chi-restraints excluded: chain N residue 435 THR Chi-restraints excluded: chain N residue 494 SER Chi-restraints excluded: chain N residue 508 ASN Chi-restraints excluded: chain N residue 516 GLU Chi-restraints excluded: chain N residue 533 GLU Chi-restraints excluded: chain N residue 538 THR Chi-restraints excluded: chain N residue 546 SER Chi-restraints excluded: chain N residue 549 SER Chi-restraints excluded: chain N residue 589 ILE Chi-restraints excluded: chain N residue 593 THR Chi-restraints excluded: chain N residue 699 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 13 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 chunk 63 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 337 optimal weight: 20.0000 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** C 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 464 GLN ** N 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.176409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134995 restraints weight = 38346.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132651 restraints weight = 55764.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134645 restraints weight = 51410.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.134472 restraints weight = 35469.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.135381 restraints weight = 33079.664| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31214 Z= 0.106 Angle : 0.586 9.030 42599 Z= 0.305 Chirality : 0.043 0.171 4746 Planarity : 0.004 0.054 5643 Dihedral : 4.654 21.986 4383 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.16 % Allowed : 25.44 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 3997 helix: -5.39 (0.09), residues: 42 sheet: -0.02 (0.14), residues: 1407 loop : -1.45 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 356 TYR 0.019 0.001 TYR E 562 PHE 0.021 0.001 PHE D 428 TRP 0.015 0.001 TRP E 706 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00251 (31207) covalent geometry : angle 0.58553 (42585) SS BOND : bond 0.00183 ( 7) SS BOND : angle 0.50774 ( 14) hydrogen bonds : bond 0.02967 ( 995) hydrogen bonds : angle 5.62479 ( 2544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.32 seconds wall clock time: 72 minutes 59.89 seconds (4379.89 seconds total)