Starting phenix.real_space_refine on Sat Mar 7 04:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.map" model { file = "/net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r10_4703/03_2026/6r10_4703.cif" } resolution = 4.3 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= 0.004 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 23944 2.51 5 N 7025 2.21 5 O 7447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38522 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "F" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1628 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 511 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 2, 'ARG:plan': 11, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "J" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 922 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLU:plan': 30, 'GLN:plan1': 10, 'ARG:plan': 19, 'TYR:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 309 Chain: "K" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 494 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 2, 'ARG:plan': 11, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "L" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 926 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLU:plan': 30, 'GLN:plan1': 10, 'ARG:plan': 19, 'TYR:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 309 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'ASP:plan': 20, 'PHE:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 35, 'GLU:plan': 26, 'GLN:plan1': 12, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 3190 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2628 Unresolved non-hydrogen dihedrals: 1714 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLU:plan': 56, 'ARG:plan': 37, 'GLN:plan1': 17, 'HIS:plan': 21, 'TYR:plan': 18, 'TRP:plan': 12, 'PHE:plan': 33, 'ASP:plan': 12, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.75, per 1000 atoms: 0.23 Number of scatterers: 38522 At special positions: 0 Unit cell: (147.56, 147.56, 252.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 4 15.00 Mg 1 11.99 O 7447 8.00 N 7025 7.00 C 23944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10530 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 41 sheets defined 57.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.632A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.933A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.381A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.601A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.987A pdb=" N TYR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 364 removed outlier: 4.433A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.855A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.010A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.322A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.588A pdb=" N ARG A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.522A pdb=" N ALA A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.646A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.968A pdb=" N GLY B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.663A pdb=" N THR B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 4.009A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.552A pdb=" N HIS B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 295 through 315 removed outlier: 4.961A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.638A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.338A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.370A pdb=" N ALA B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 508 through 533 removed outlier: 4.170A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.660A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 552 removed outlier: 3.863A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 562 through 577 removed outlier: 4.179A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.548A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.539A pdb=" N HIS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.210A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.924A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.405A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.750A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 478 through 494 removed outlier: 3.934A pdb=" N LEU C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 531 removed outlier: 4.306A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.590A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 573 removed outlier: 3.785A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.800A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 4.235A pdb=" N LEU D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.057A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 249 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.708A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.620A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.761A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.709A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 400 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.725A pdb=" N ARG D 420 " --> pdb=" O ASP D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.523A pdb=" N ILE D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 227 through 248 removed outlier: 3.922A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 272 removed outlier: 3.754A pdb=" N ALA E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.711A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.644A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 397 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 442 Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.783A pdb=" N GLU E 450 " --> pdb=" O PRO E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 462 removed outlier: 3.509A pdb=" N TYR E 462 " --> pdb=" O HIS E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 141 Processing helix chain 'F' and resid 159 through 170 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.982A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 212 Processing helix chain 'F' and resid 233 through 248 removed outlier: 3.609A pdb=" N VAL F 241 " --> pdb=" O MET F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 removed outlier: 4.004A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG F 274 " --> pdb=" O ILE F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.157A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 345 removed outlier: 3.887A pdb=" N HIS F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 345' Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.738A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.849A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.531A pdb=" N LEU F 404 " --> pdb=" O GLU F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 407 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 462 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.533A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 123 through 169 removed outlier: 3.811A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 208 Processing helix chain 'H' and resid 9 through 16 Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 55 through 63 removed outlier: 4.356A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 Processing helix chain 'I' and resid 19 through 103 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 3 through 97 Proline residue: J 95 - end of helix Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.821A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.483A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'J' and resid 167 through 187 removed outlier: 5.562A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 106 Processing helix chain 'K' and resid 109 through 119 removed outlier: 3.891A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 94 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 126 through 131 removed outlier: 4.155A pdb=" N HIS L 130 " --> pdb=" O GLU L 126 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 131' Processing helix chain 'L' and resid 131 through 137 Processing helix chain 'L' and resid 166 through 188 removed outlier: 5.115A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY L 188 " --> pdb=" O GLN L 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.915A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 28 removed outlier: 3.676A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 43 Processing helix chain 'M' and resid 44 through 48 Processing helix chain 'M' and resid 53 through 69 Processing helix chain 'M' and resid 78 through 86 Processing helix chain 'M' and resid 88 through 106 removed outlier: 4.555A pdb=" N ASP M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 removed outlier: 3.723A pdb=" N GLU M 129 " --> pdb=" O ARG M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'M' and resid 162 through 182 Processing helix chain 'M' and resid 187 through 207 removed outlier: 3.671A pdb=" N TYR M 191 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 218 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 243 Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 279 Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'N' and resid 13 through 27 Processing helix chain 'N' and resid 46 through 71 Processing helix chain 'N' and resid 83 through 118 Proline residue: N 93 - end of helix removed outlier: 3.543A pdb=" N GLN N 106 " --> pdb=" O THR N 102 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 129 removed outlier: 3.728A pdb=" N LEU N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.805A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 175 Processing helix chain 'N' and resid 184 through 198 Processing helix chain 'N' and resid 212 through 268 Proline residue: N 228 - end of helix removed outlier: 5.942A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 296 Processing helix chain 'N' and resid 329 through 335 removed outlier: 3.940A pdb=" N LEU N 333 " --> pdb=" O PRO N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 363 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 385 Processing helix chain 'N' and resid 399 through 425 removed outlier: 4.079A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 458 through 489 removed outlier: 4.303A pdb=" N LEU N 462 " --> pdb=" O LYS N 458 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY N 471 " --> pdb=" O SER N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 Processing helix chain 'N' and resid 521 through 541 removed outlier: 4.444A pdb=" N GLY N 526 " --> pdb=" O GLY N 522 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU N 527 " --> pdb=" O TRP N 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 560 removed outlier: 3.767A pdb=" N ILE N 551 " --> pdb=" O MET N 547 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 587 removed outlier: 4.035A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 632 removed outlier: 5.224A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.880A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 4.097A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 10 through 48 removed outlier: 3.727A pdb=" N LEU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'Q' and resid 10 through 48 removed outlier: 4.153A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 63 through 79 Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.982A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 removed outlier: 3.655A pdb=" N LEU R 56 " --> pdb=" O PHE R 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 11 through 48 removed outlier: 4.181A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 63 through 80 Processing helix chain 'T' and resid 10 through 48 removed outlier: 3.642A pdb=" N LEU T 14 " --> pdb=" O LEU T 10 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 10 through 48 removed outlier: 4.127A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 63 through 80 Processing helix chain 'V' and resid 10 through 48 removed outlier: 4.402A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 62 through 80 removed outlier: 4.266A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 48 removed outlier: 4.129A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 removed outlier: 3.540A pdb=" N ALA W 55 " --> pdb=" O ASN W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 80 Processing helix chain 'X' and resid 13 through 48 removed outlier: 4.021A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.777A pdb=" N ALA X 55 " --> pdb=" O ASN X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 80 removed outlier: 4.461A pdb=" N VAL X 66 " --> pdb=" O PRO X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 46 removed outlier: 4.036A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 80 Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.509A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA Z 16 " --> pdb=" O ARG Z 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL Z 17 " --> pdb=" O GLY Z 13 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 63 through 80 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.600A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 9 current: chain 'F' and resid 72 through 76 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.600A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL F 50 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 42 through 51 current: chain 'A' and resid 27 through 30 removed outlier: 5.559A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 48 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 9 current: chain 'F' and resid 72 through 76 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.271A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.271A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 224 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 384 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 226 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 143 through 145 removed outlier: 5.969A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AA8, first strand: chain 'J' and resid 142 through 144 removed outlier: 6.415A pdb=" N LEU J 121 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E 18 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE E 14 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 83 through 84 removed outlier: 5.799A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL B 250 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE B 288 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 252 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB3, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.834A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.627A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 197 through 198 removed outlier: 4.163A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 383 through 384 removed outlier: 7.371A pdb=" N VAL B 384 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE B 226 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 10 removed outlier: 5.877A pdb=" N ILE C 6 " --> pdb=" O LYS C 17 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 17 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C 26 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 27 " --> pdb=" O THR C 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.394A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 291 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL C 381 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 322 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 383 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 324 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 197 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.394A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 291 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL C 250 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 288 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 252 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 290 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY C 254 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 251 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP C 325 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 253 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL C 381 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 322 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 383 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA C 324 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 224 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 117 through 118 Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.514A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AC6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC7, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.481A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 188 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE D 256 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 190 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR D 258 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA D 192 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.481A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 188 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE D 256 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D 190 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR D 258 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA D 192 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE D 152 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.425A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AD2, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.479A pdb=" N GLN E 129 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.530A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 253 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE E 311 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL E 255 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE E 313 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU E 257 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N SER E 315 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.616A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 217 through 222 removed outlier: 6.684A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 299 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AD8, first strand: chain 'H' and resid 2 through 4 removed outlier: 4.209A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 141 through 144 removed outlier: 6.398A pdb=" N LEU L 121 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.913A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA N 270 " --> pdb=" O ALA N 277 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.913A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA N 11 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL N 302 " --> pdb=" O ALA N 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 141 through 145 Processing sheet with id=AE4, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AE5, first strand: chain 'N' and resid 389 through 391 2717 hydrogen bonds defined for protein. 7950 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: 9.12 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12041 1.34 - 1.45: 5854 1.45 - 1.57: 20935 1.57 - 1.69: 7 1.69 - 1.81: 190 Bond restraints: 39027 Sorted by residual: bond pdb=" C LEU E 355 " pdb=" N PRO E 356 " ideal model delta sigma weight residual 1.331 1.371 -0.040 7.90e-03 1.60e+04 2.56e+01 bond pdb=" C PHE C 48 " pdb=" N VAL C 49 " ideal model delta sigma weight residual 1.329 1.287 0.042 1.69e-02 3.50e+03 6.08e+00 bond pdb=" C ASP D 353 " pdb=" N PRO D 354 " ideal model delta sigma weight residual 1.336 1.312 0.024 9.80e-03 1.04e+04 5.81e+00 bond pdb=" C GLY F 157 " pdb=" N LEU F 158 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.83e-02 1.25e+03 5.78e+00 bond pdb=" C VAL E 189 " pdb=" N VAL E 190 " ideal model delta sigma weight residual 1.329 1.296 0.033 1.46e-02 4.69e+03 5.18e+00 ... (remaining 39022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 52610 3.44 - 6.88: 546 6.88 - 10.32: 65 10.32 - 13.76: 8 13.76 - 17.20: 1 Bond angle restraints: 53230 Sorted by residual: angle pdb=" C THR F 371 " pdb=" N ARG F 372 " pdb=" CA ARG F 372 " ideal model delta sigma weight residual 122.19 134.33 -12.14 2.30e+00 1.89e-01 2.79e+01 angle pdb=" C LEU E 361 " pdb=" N MET E 362 " pdb=" CA MET E 362 " ideal model delta sigma weight residual 126.45 135.72 -9.27 1.77e+00 3.19e-01 2.75e+01 angle pdb=" C GLY C 233 " pdb=" N LYS C 234 " pdb=" CA LYS C 234 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ASP F 318 " pdb=" N ASP F 319 " pdb=" CA ASP F 319 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.54e+01 angle pdb=" C GLU D 22 " pdb=" N ASN D 23 " pdb=" CA ASN D 23 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.47e+01 ... (remaining 53225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 23133 35.80 - 71.60: 95 71.60 - 107.40: 6 107.40 - 143.20: 1 143.20 - 179.00: 1 Dihedral angle restraints: 23236 sinusoidal: 6764 harmonic: 16472 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 119.00 -179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA VAL H 3 " pdb=" C VAL H 3 " pdb=" N ILE H 4 " pdb=" CA ILE H 4 " ideal model delta harmonic sigma weight residual 180.00 145.56 34.44 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA GLY C 142 " pdb=" C GLY C 142 " pdb=" N PHE C 143 " pdb=" CA PHE C 143 " ideal model delta harmonic sigma weight residual -180.00 -146.22 -33.78 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 23233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 5607 0.088 - 0.176: 623 0.176 - 0.264: 36 0.264 - 0.353: 3 0.353 - 0.441: 4 Chirality restraints: 6273 Sorted by residual: chirality pdb=" CB ILE E 392 " pdb=" CA ILE E 392 " pdb=" CG1 ILE E 392 " pdb=" CG2 ILE E 392 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL B 378 " pdb=" CA VAL B 378 " pdb=" CG1 VAL B 378 " pdb=" CG2 VAL B 378 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 6270 not shown) Planarity restraints: 7224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 234 " -0.021 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C LYS C 234 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS C 234 " -0.026 2.00e-02 2.50e+03 pdb=" N THR C 235 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO D 356 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 28 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C CYS B 28 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS B 28 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B 29 " -0.017 2.00e-02 2.50e+03 ... (remaining 7221 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1351 2.70 - 3.25: 37829 3.25 - 3.80: 63793 3.80 - 4.35: 72492 4.35 - 4.90: 123401 Nonbonded interactions: 298866 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O3B ADP A 602 " model vdw 2.155 2.170 nonbonded pdb=" O PRO C 386 " pdb=" OH TYR E 331 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU A 257 " pdb=" OG SER A 326 " model vdw 2.241 3.040 nonbonded pdb=" OG SER D 431 " pdb=" OE1 GLU D 434 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP A 446 " pdb=" OH TYR A 513 " model vdw 2.263 3.040 ... (remaining 298861 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 1 through 577) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 2 through 187) } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 36.160 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 0.081 39027 Z= 0.297 Angle : 0.964 17.202 53230 Z= 0.531 Chirality : 0.055 0.441 6273 Planarity : 0.007 0.075 7224 Dihedral : 9.708 178.996 12706 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.74 (0.09), residues: 5790 helix: -1.95 (0.07), residues: 3133 sheet: -2.39 (0.20), residues: 530 loop : -3.15 (0.11), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 280 TYR 0.033 0.003 TYR F 383 PHE 0.036 0.003 PHE G 130 TRP 0.038 0.004 TRP A 438 HIS 0.014 0.002 HIS F 458 Details of bonding type rmsd covalent geometry : bond 0.00651 (39027) covalent geometry : angle 0.96392 (53230) hydrogen bonds : bond 0.09652 ( 2678) hydrogen bonds : angle 5.99340 ( 7950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1027 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 VAL cc_start: 0.8972 (t) cc_final: 0.8733 (m) REVERT: A 35 LEU cc_start: 0.8111 (mp) cc_final: 0.7904 (mp) REVERT: A 92 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8438 (tm-30) REVERT: A 102 ILE cc_start: 0.9129 (mt) cc_final: 0.8848 (mp) REVERT: A 196 GLN cc_start: 0.8803 (tt0) cc_final: 0.8478 (tm-30) REVERT: A 332 GLU cc_start: 0.8862 (tt0) cc_final: 0.8184 (tm-30) REVERT: A 336 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8667 (mm-30) REVERT: A 343 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8670 (mm-30) REVERT: A 459 GLN cc_start: 0.8918 (tp40) cc_final: 0.7964 (tp40) REVERT: A 478 ASP cc_start: 0.8622 (m-30) cc_final: 0.7886 (p0) REVERT: A 480 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8482 (mp0) REVERT: A 492 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8853 (mm-30) REVERT: A 527 GLU cc_start: 0.8853 (pt0) cc_final: 0.8611 (tm-30) REVERT: A 538 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8347 (tp30) REVERT: B 81 ASN cc_start: 0.9306 (t0) cc_final: 0.9088 (t0) REVERT: B 133 MET cc_start: 0.8781 (ttt) cc_final: 0.7947 (mtt) REVERT: B 147 ILE cc_start: 0.9036 (mt) cc_final: 0.8833 (tt) REVERT: B 179 THR cc_start: 0.7849 (m) cc_final: 0.7466 (p) REVERT: B 251 VAL cc_start: 0.9605 (t) cc_final: 0.9371 (p) REVERT: B 287 LEU cc_start: 0.8551 (tt) cc_final: 0.8289 (mp) REVERT: B 291 THR cc_start: 0.9140 (p) cc_final: 0.8840 (p) REVERT: B 328 SER cc_start: 0.9427 (m) cc_final: 0.9020 (p) REVERT: B 342 GLU cc_start: 0.9021 (mp0) cc_final: 0.8789 (mp0) REVERT: B 343 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 391 MET cc_start: 0.7733 (mmt) cc_final: 0.6447 (mmp) REVERT: B 417 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8340 (tpt90) REVERT: B 481 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8457 (tpp80) REVERT: B 541 GLN cc_start: 0.9239 (pt0) cc_final: 0.8783 (pm20) REVERT: B 546 GLU cc_start: 0.9185 (tt0) cc_final: 0.8646 (tm-30) REVERT: B 550 ARG cc_start: 0.8836 (mmt-90) cc_final: 0.8412 (ptt-90) REVERT: B 558 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8916 (tm-30) REVERT: C 3 GLN cc_start: 0.8323 (tt0) cc_final: 0.8084 (tm-30) REVERT: C 24 MET cc_start: 0.8270 (mmm) cc_final: 0.7952 (tpp) REVERT: C 74 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8637 (tt0) REVERT: C 101 TYR cc_start: 0.8491 (m-80) cc_final: 0.8163 (m-80) REVERT: C 251 VAL cc_start: 0.9215 (t) cc_final: 0.8890 (m) REVERT: C 268 GLU cc_start: 0.9273 (pt0) cc_final: 0.8414 (tm-30) REVERT: C 282 MET cc_start: 0.8911 (tpt) cc_final: 0.8592 (tpp) REVERT: C 287 LEU cc_start: 0.8784 (pp) cc_final: 0.8440 (tt) REVERT: C 288 ILE cc_start: 0.8897 (mt) cc_final: 0.8672 (mm) REVERT: C 290 ASN cc_start: 0.9190 (t0) cc_final: 0.8656 (t0) REVERT: C 300 GLU cc_start: 0.9486 (tt0) cc_final: 0.8867 (tp30) REVERT: C 304 TYR cc_start: 0.9069 (m-80) cc_final: 0.8794 (m-80) REVERT: C 322 LEU cc_start: 0.9207 (tt) cc_final: 0.8898 (tt) REVERT: C 344 MET cc_start: 0.9128 (mmm) cc_final: 0.8882 (mmm) REVERT: C 410 ASP cc_start: 0.8302 (m-30) cc_final: 0.7783 (m-30) REVERT: C 450 LEU cc_start: 0.8849 (tp) cc_final: 0.8085 (tt) REVERT: C 456 GLU cc_start: 0.8912 (pp20) cc_final: 0.8138 (tp30) REVERT: C 480 GLU cc_start: 0.8738 (pt0) cc_final: 0.8498 (pt0) REVERT: C 498 ASN cc_start: 0.8558 (t0) cc_final: 0.8306 (t0) REVERT: C 538 GLU cc_start: 0.9428 (tt0) cc_final: 0.9202 (tm-30) REVERT: C 558 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7638 (mp0) REVERT: C 567 MET cc_start: 0.8271 (mtt) cc_final: 0.7775 (tpp) REVERT: D 15 SER cc_start: 0.8515 (t) cc_final: 0.8283 (p) REVERT: D 49 GLU cc_start: 0.8993 (tt0) cc_final: 0.8759 (mt-10) REVERT: D 62 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8436 (mm-30) REVERT: D 103 LEU cc_start: 0.8867 (mt) cc_final: 0.8609 (mt) REVERT: D 128 GLU cc_start: 0.7740 (pt0) cc_final: 0.7085 (mt-10) REVERT: D 149 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8377 (ptpt) REVERT: D 154 SER cc_start: 0.9140 (t) cc_final: 0.8788 (p) REVERT: D 182 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7748 (pm20) REVERT: D 206 GLN cc_start: 0.8967 (tt0) cc_final: 0.8726 (tp40) REVERT: D 237 MET cc_start: 0.9168 (mmt) cc_final: 0.8454 (mtp) REVERT: D 290 ASP cc_start: 0.9285 (t0) cc_final: 0.8568 (t0) REVERT: D 316 MET cc_start: 0.9159 (mtm) cc_final: 0.8818 (mtt) REVERT: D 320 ASP cc_start: 0.8683 (p0) cc_final: 0.8473 (p0) REVERT: D 333 THR cc_start: 0.9616 (p) cc_final: 0.9353 (t) REVERT: D 334 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9069 (mm-30) REVERT: D 338 GLN cc_start: 0.9163 (tt0) cc_final: 0.8196 (tp40) REVERT: D 348 ILE cc_start: 0.9145 (mt) cc_final: 0.8933 (mp) REVERT: D 364 ASN cc_start: 0.9349 (m110) cc_final: 0.8933 (t0) REVERT: D 374 ASP cc_start: 0.8497 (p0) cc_final: 0.7733 (p0) REVERT: D 425 GLN cc_start: 0.8599 (tt0) cc_final: 0.8203 (tt0) REVERT: E 58 GLN cc_start: 0.9227 (tt0) cc_final: 0.8837 (tm-30) REVERT: E 77 GLU cc_start: 0.8154 (pt0) cc_final: 0.7928 (pt0) REVERT: E 166 GLN cc_start: 0.9337 (tt0) cc_final: 0.9134 (tt0) REVERT: E 274 ARG cc_start: 0.8690 (mtm-85) cc_final: 0.8232 (ptm-80) REVERT: E 280 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7425 (tpp80) REVERT: E 318 ASP cc_start: 0.9032 (t0) cc_final: 0.8741 (t0) REVERT: E 343 LEU cc_start: 0.8978 (mm) cc_final: 0.8720 (mp) REVERT: E 345 ARG cc_start: 0.9189 (mtm-85) cc_final: 0.8787 (mmm160) REVERT: E 364 ASN cc_start: 0.8244 (t0) cc_final: 0.8013 (t0) REVERT: E 372 ARG cc_start: 0.8497 (ttm170) cc_final: 0.8208 (ttm-80) REVERT: E 416 ASP cc_start: 0.8934 (t0) cc_final: 0.8653 (t0) REVERT: E 453 ARG cc_start: 0.8069 (mpt180) cc_final: 0.7856 (mpt180) REVERT: F 34 ASP cc_start: 0.8106 (p0) cc_final: 0.7785 (t0) REVERT: F 46 GLN cc_start: 0.8640 (tt0) cc_final: 0.8416 (tp40) REVERT: F 60 PHE cc_start: 0.9148 (m-10) cc_final: 0.8416 (m-80) REVERT: F 61 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8410 (tm-30) REVERT: F 120 ASN cc_start: 0.9313 (t0) cc_final: 0.8818 (t0) REVERT: F 156 SER cc_start: 0.9114 (m) cc_final: 0.8553 (p) REVERT: F 174 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8194 (mtp85) REVERT: F 207 GLU cc_start: 0.8827 (tp30) cc_final: 0.8489 (tm-30) REVERT: F 227 PRO cc_start: 0.8489 (Cg_exo) cc_final: 0.7906 (Cg_endo) REVERT: F 305 LYS cc_start: 0.9487 (mptm) cc_final: 0.9257 (tttt) REVERT: F 307 SER cc_start: 0.8608 (p) cc_final: 0.8170 (m) REVERT: F 316 MET cc_start: 0.9063 (mtm) cc_final: 0.8782 (mtm) REVERT: F 318 ASP cc_start: 0.9198 (t0) cc_final: 0.8633 (p0) REVERT: F 342 GLU cc_start: 0.9422 (tt0) cc_final: 0.9183 (tp30) REVERT: F 374 ASP cc_start: 0.9082 (p0) cc_final: 0.8346 (t0) REVERT: F 376 LYS cc_start: 0.8586 (mttt) cc_final: 0.8300 (mttt) REVERT: F 410 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7540 (mpt180) REVERT: F 413 GLN cc_start: 0.8744 (mt0) cc_final: 0.8429 (mt0) REVERT: F 446 LEU cc_start: 0.9110 (mt) cc_final: 0.8707 (tp) REVERT: F 454 ILE cc_start: 0.8449 (mt) cc_final: 0.8132 (tt) REVERT: G 5 SER cc_start: 0.8629 (m) cc_final: 0.8412 (p) REVERT: G 13 GLN cc_start: 0.9297 (tt0) cc_final: 0.8599 (tm-30) REVERT: G 30 LYS cc_start: 0.9267 (mtpp) cc_final: 0.8930 (mttp) REVERT: G 31 LYS cc_start: 0.8988 (tttm) cc_final: 0.8365 (tmtt) REVERT: G 50 ARG cc_start: 0.8906 (tpp-160) cc_final: 0.8339 (ttt90) REVERT: G 55 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8167 (tm-30) REVERT: G 58 LYS cc_start: 0.8860 (ttpm) cc_final: 0.8572 (tppt) REVERT: G 93 VAL cc_start: 0.8715 (t) cc_final: 0.8417 (m) REVERT: G 146 ARG cc_start: 0.8856 (ptp90) cc_final: 0.8282 (ptp90) REVERT: G 159 ARG cc_start: 0.8667 (ptt180) cc_final: 0.8382 (ttp80) REVERT: G 180 GLN cc_start: 0.8587 (mt0) cc_final: 0.8318 (mt0) REVERT: G 183 LEU cc_start: 0.9069 (mt) cc_final: 0.8694 (tt) REVERT: G 185 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8469 (tp40) REVERT: H 14 ARG cc_start: 0.8692 (mtt180) cc_final: 0.7827 (tpt170) REVERT: H 60 GLU cc_start: 0.7280 (pp20) cc_final: 0.6330 (mm-30) REVERT: H 90 MET cc_start: 0.8444 (mmp) cc_final: 0.7031 (ttt) REVERT: H 96 LYS cc_start: 0.9322 (tttp) cc_final: 0.9073 (ttpp) REVERT: H 97 THR cc_start: 0.8873 (m) cc_final: 0.8206 (p) outliers start: 3 outliers final: 1 residues processed: 1029 average time/residue: 0.2801 time to fit residues: 441.1841 Evaluate side-chains 618 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 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 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 290 ASN B 316 GLN B 397 GLN B 477 GLN C 238 GLN C 283 HIS C 316 GLN C 459 GLN D 58 GLN D 161 ASN D 310 GLN E 129 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 252 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN E 458 HIS ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 425 GLN G 3 GLN G 180 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.113088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088512 restraints weight = 112121.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090620 restraints weight = 69407.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091402 restraints weight = 44473.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.092774 restraints weight = 31116.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093223 restraints weight = 19646.181| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39027 Z= 0.190 Angle : 0.670 14.884 53230 Z= 0.349 Chirality : 0.044 0.223 6273 Planarity : 0.005 0.057 7224 Dihedral : 6.258 156.988 6204 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -1.41 (0.10), residues: 5790 helix: 0.40 (0.09), residues: 3183 sheet: -2.16 (0.20), residues: 578 loop : -2.72 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 231 TYR 0.024 0.002 TYR E 263 PHE 0.036 0.002 PHE B 141 TRP 0.023 0.002 TRP A 330 HIS 0.008 0.002 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00419 (39027) covalent geometry : angle 0.66982 (53230) hydrogen bonds : bond 0.03776 ( 2678) hydrogen bonds : angle 4.51062 ( 7950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 776 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 102 ILE cc_start: 0.9048 (mt) cc_final: 0.8722 (tt) REVERT: A 300 GLU cc_start: 0.7612 (tt0) cc_final: 0.7374 (tt0) REVERT: A 424 TRP cc_start: 0.8907 (t60) cc_final: 0.8663 (t60) REVERT: A 456 GLU cc_start: 0.8254 (pp20) cc_final: 0.7981 (tm-30) REVERT: B 60 VAL cc_start: 0.9316 (t) cc_final: 0.8858 (m) REVERT: B 81 ASN cc_start: 0.8691 (t0) cc_final: 0.8379 (t0) REVERT: B 179 THR cc_start: 0.8345 (m) cc_final: 0.7910 (p) REVERT: B 212 LEU cc_start: 0.9564 (mt) cc_final: 0.9360 (mt) REVERT: B 311 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 328 SER cc_start: 0.9170 (m) cc_final: 0.8740 (t) REVERT: B 341 LEU cc_start: 0.9366 (mt) cc_final: 0.8848 (mm) REVERT: B 391 MET cc_start: 0.7181 (mmt) cc_final: 0.6730 (mmp) REVERT: B 480 GLU cc_start: 0.8617 (mp0) cc_final: 0.8231 (pm20) REVERT: B 516 MET cc_start: 0.8048 (mtp) cc_final: 0.7669 (mtm) REVERT: C 24 MET cc_start: 0.8641 (mmm) cc_final: 0.8404 (tpp) REVERT: C 26 ASP cc_start: 0.8140 (m-30) cc_final: 0.7837 (m-30) REVERT: C 184 TYR cc_start: 0.8643 (p90) cc_final: 0.8235 (p90) REVERT: C 261 GLU cc_start: 0.8779 (mp0) cc_final: 0.8279 (mp0) REVERT: C 282 MET cc_start: 0.8198 (tpt) cc_final: 0.7628 (tpt) REVERT: C 304 TYR cc_start: 0.8475 (m-80) cc_final: 0.8015 (m-80) REVERT: C 347 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7391 (mt-10) REVERT: C 410 ASP cc_start: 0.8120 (m-30) cc_final: 0.7755 (m-30) REVERT: C 456 GLU cc_start: 0.8586 (pp20) cc_final: 0.8232 (tp30) REVERT: C 557 GLU cc_start: 0.8115 (pm20) cc_final: 0.7691 (pm20) REVERT: C 558 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6650 (mp0) REVERT: D 154 SER cc_start: 0.9467 (t) cc_final: 0.9154 (p) REVERT: D 237 MET cc_start: 0.9045 (mmt) cc_final: 0.8614 (mmm) REVERT: D 264 CYS cc_start: 0.7918 (t) cc_final: 0.7461 (t) REVERT: D 333 THR cc_start: 0.9289 (p) cc_final: 0.9067 (t) REVERT: D 334 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 338 GLN cc_start: 0.8398 (tt0) cc_final: 0.8151 (tp40) REVERT: D 348 ILE cc_start: 0.9366 (mt) cc_final: 0.9062 (mp) REVERT: D 374 ASP cc_start: 0.7925 (p0) cc_final: 0.7453 (p0) REVERT: D 425 GLN cc_start: 0.8286 (tt0) cc_final: 0.7988 (tp-100) REVERT: D 428 GLN cc_start: 0.7209 (tt0) cc_final: 0.6877 (tt0) REVERT: E 207 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7268 (tm-30) REVERT: E 349 TYR cc_start: 0.7674 (t80) cc_final: 0.6388 (t80) REVERT: E 408 ASP cc_start: 0.8167 (m-30) cc_final: 0.7773 (m-30) REVERT: E 437 GLN cc_start: 0.8416 (pt0) cc_final: 0.8082 (mm-40) REVERT: F 60 PHE cc_start: 0.9166 (m-10) cc_final: 0.8594 (m-80) REVERT: F 120 ASN cc_start: 0.9418 (t0) cc_final: 0.8997 (t0) REVERT: F 170 GLN cc_start: 0.7322 (pm20) cc_final: 0.5876 (pp30) REVERT: F 287 MET cc_start: 0.8568 (ttm) cc_final: 0.8108 (ttm) REVERT: F 323 HIS cc_start: 0.8597 (t-90) cc_final: 0.7134 (t-90) REVERT: F 416 ASP cc_start: 0.8535 (p0) cc_final: 0.8321 (t0) REVERT: F 423 ILE cc_start: 0.9401 (mt) cc_final: 0.9191 (mt) REVERT: G 15 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7661 (mmm-85) REVERT: G 31 LYS cc_start: 0.8899 (tttm) cc_final: 0.8652 (tttm) REVERT: G 144 GLU cc_start: 0.8598 (tp30) cc_final: 0.8318 (tp30) REVERT: G 153 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7405 (tp30) REVERT: G 183 LEU cc_start: 0.9288 (mt) cc_final: 0.8976 (tt) REVERT: G 198 LYS cc_start: 0.8846 (tttt) cc_final: 0.8561 (tttp) REVERT: H 14 ARG cc_start: 0.8537 (mtt180) cc_final: 0.8028 (mmm-85) REVERT: H 60 GLU cc_start: 0.7326 (pp20) cc_final: 0.6417 (mm-30) REVERT: H 89 TYR cc_start: 0.8796 (t80) cc_final: 0.8349 (t80) outliers start: 2 outliers final: 0 residues processed: 778 average time/residue: 0.2570 time to fit residues: 313.3744 Evaluate side-chains 529 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 46 optimal weight: 9.9990 chunk 443 optimal weight: 8.9990 chunk 427 optimal weight: 40.0000 chunk 509 optimal weight: 50.0000 chunk 447 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 320 optimal weight: 40.0000 chunk 231 optimal weight: 9.9990 chunk 496 optimal weight: 9.9990 chunk 566 optimal weight: 9.9990 overall best weight: 7.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 310 GLN E 375 HIS E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 425 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.112032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087193 restraints weight = 114513.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089242 restraints weight = 71741.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.089656 restraints weight = 44532.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090089 restraints weight = 37334.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091636 restraints weight = 29389.671| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 39027 Z= 0.219 Angle : 0.680 15.535 53230 Z= 0.353 Chirality : 0.045 0.234 6273 Planarity : 0.005 0.072 7224 Dihedral : 5.812 125.191 6204 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: -0.40 (0.11), residues: 5790 helix: 1.41 (0.09), residues: 3196 sheet: -2.04 (0.20), residues: 587 loop : -2.55 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 210 TYR 0.019 0.002 TYR E 386 PHE 0.025 0.002 PHE B 141 TRP 0.028 0.002 TRP A 330 HIS 0.006 0.002 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00482 (39027) covalent geometry : angle 0.68006 (53230) hydrogen bonds : bond 0.03693 ( 2678) hydrogen bonds : angle 4.31061 ( 7950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7340 (mmp80) cc_final: 0.6524 (mmp80) REVERT: A 96 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 102 ILE cc_start: 0.9000 (mt) cc_final: 0.8745 (tt) REVERT: A 332 GLU cc_start: 0.7490 (pp20) cc_final: 0.7066 (tm-30) REVERT: A 424 TRP cc_start: 0.8854 (t60) cc_final: 0.8422 (t60) REVERT: A 456 GLU cc_start: 0.8268 (pp20) cc_final: 0.8022 (tm-30) REVERT: A 478 ASP cc_start: 0.7766 (p0) cc_final: 0.7557 (p0) REVERT: A 480 GLU cc_start: 0.8942 (mp0) cc_final: 0.8283 (mp0) REVERT: A 553 TYR cc_start: 0.7525 (m-10) cc_final: 0.7058 (m-10) REVERT: A 563 PHE cc_start: 0.8433 (t80) cc_final: 0.8164 (t80) REVERT: B 81 ASN cc_start: 0.8754 (t0) cc_final: 0.8441 (t0) REVERT: B 179 THR cc_start: 0.8361 (m) cc_final: 0.8076 (p) REVERT: B 212 LEU cc_start: 0.9544 (mt) cc_final: 0.9301 (mt) REVERT: B 311 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8611 (mt-10) REVERT: B 328 SER cc_start: 0.9256 (m) cc_final: 0.8732 (t) REVERT: B 391 MET cc_start: 0.7134 (mmt) cc_final: 0.6516 (mmp) REVERT: B 480 GLU cc_start: 0.8627 (mp0) cc_final: 0.8363 (pm20) REVERT: B 495 LEU cc_start: 0.9377 (mt) cc_final: 0.9103 (mp) REVERT: B 516 MET cc_start: 0.8205 (mtp) cc_final: 0.7837 (mtm) REVERT: B 546 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7161 (tm-30) REVERT: B 547 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7004 (ttm110) REVERT: B 550 ARG cc_start: 0.7334 (ptt-90) cc_final: 0.6779 (ptt180) REVERT: C 24 MET cc_start: 0.8600 (mmm) cc_final: 0.8122 (tpp) REVERT: C 261 GLU cc_start: 0.8812 (mp0) cc_final: 0.7732 (mp0) REVERT: C 282 MET cc_start: 0.8187 (tpt) cc_final: 0.7621 (tpt) REVERT: C 304 TYR cc_start: 0.8559 (m-80) cc_final: 0.8141 (m-80) REVERT: C 456 GLU cc_start: 0.8639 (pp20) cc_final: 0.8345 (tp30) REVERT: C 558 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6511 (mp0) REVERT: D 154 SER cc_start: 0.9475 (t) cc_final: 0.9266 (p) REVERT: D 200 GLU cc_start: 0.8268 (pt0) cc_final: 0.8067 (pt0) REVERT: D 237 MET cc_start: 0.9085 (mmt) cc_final: 0.8737 (mmm) REVERT: D 374 ASP cc_start: 0.7850 (p0) cc_final: 0.7417 (p0) REVERT: D 428 GLN cc_start: 0.7266 (tt0) cc_final: 0.6929 (mt0) REVERT: D 445 MET cc_start: 0.8594 (ttt) cc_final: 0.8378 (ttt) REVERT: E 437 GLN cc_start: 0.8462 (pt0) cc_final: 0.8209 (mm-40) REVERT: F 170 GLN cc_start: 0.7345 (pm20) cc_final: 0.6496 (pp30) REVERT: F 260 MET cc_start: 0.9342 (mmp) cc_final: 0.9052 (mmp) REVERT: F 323 HIS cc_start: 0.8566 (t-90) cc_final: 0.8171 (t-90) REVERT: G 15 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7554 (mmm-85) REVERT: G 19 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7661 (ptp-110) REVERT: G 22 GLN cc_start: 0.7684 (tp40) cc_final: 0.7474 (tm-30) REVERT: G 26 ASP cc_start: 0.7897 (t70) cc_final: 0.7295 (t0) REVERT: G 31 LYS cc_start: 0.8999 (tttm) cc_final: 0.8748 (tttm) REVERT: G 139 ARG cc_start: 0.9201 (tmm-80) cc_final: 0.8988 (tmm-80) REVERT: G 144 GLU cc_start: 0.8560 (tp30) cc_final: 0.8297 (tp30) REVERT: G 153 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7398 (tp30) REVERT: G 183 LEU cc_start: 0.9260 (mt) cc_final: 0.9044 (tt) REVERT: H 14 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8051 (mmm-85) REVERT: H 57 ARG cc_start: 0.8472 (mpt-90) cc_final: 0.7981 (mpt-90) REVERT: H 60 GLU cc_start: 0.7497 (pp20) cc_final: 0.6473 (mm-30) REVERT: H 89 TYR cc_start: 0.8578 (t80) cc_final: 0.8289 (t80) REVERT: H 97 THR cc_start: 0.8619 (p) cc_final: 0.8039 (p) outliers start: 1 outliers final: 0 residues processed: 683 average time/residue: 0.2623 time to fit residues: 280.6052 Evaluate side-chains 497 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 420 optimal weight: 50.0000 chunk 254 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 458 optimal weight: 0.4980 chunk 150 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 355 optimal weight: 50.0000 chunk 440 optimal weight: 40.0000 chunk 59 optimal weight: 20.0000 chunk 375 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 overall best weight: 10.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 316 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 375 HIS E 413 GLN E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 413 GLN G 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086037 restraints weight = 115345.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087770 restraints weight = 73363.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.088307 restraints weight = 47097.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088879 restraints weight = 39609.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.089469 restraints weight = 29893.166| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 39027 Z= 0.260 Angle : 0.713 16.785 53230 Z= 0.369 Chirality : 0.046 0.252 6273 Planarity : 0.005 0.050 7224 Dihedral : 5.666 98.522 6204 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.06 (0.12), residues: 5790 helix: 1.88 (0.09), residues: 3195 sheet: -2.07 (0.21), residues: 576 loop : -2.46 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 210 TYR 0.018 0.002 TYR E 386 PHE 0.051 0.002 PHE C 269 TRP 0.033 0.002 TRP A 330 HIS 0.006 0.002 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00577 (39027) covalent geometry : angle 0.71313 (53230) hydrogen bonds : bond 0.03747 ( 2678) hydrogen bonds : angle 4.31152 ( 7950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 630 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9055 (mt) cc_final: 0.8755 (tt) REVERT: A 282 MET cc_start: 0.8653 (tpt) cc_final: 0.8393 (tpt) REVERT: A 332 GLU cc_start: 0.7939 (pp20) cc_final: 0.5997 (tm-30) REVERT: A 353 TYR cc_start: 0.7700 (p90) cc_final: 0.7310 (p90) REVERT: A 393 GLU cc_start: 0.8290 (mp0) cc_final: 0.7945 (mp0) REVERT: A 424 TRP cc_start: 0.8727 (t60) cc_final: 0.8231 (t60) REVERT: A 456 GLU cc_start: 0.8284 (pp20) cc_final: 0.8020 (tm-30) REVERT: A 480 GLU cc_start: 0.8825 (mp0) cc_final: 0.8337 (mp0) REVERT: B 81 ASN cc_start: 0.8778 (t0) cc_final: 0.8522 (t0) REVERT: B 209 MET cc_start: 0.7993 (ptt) cc_final: 0.7782 (ptt) REVERT: B 212 LEU cc_start: 0.9520 (mt) cc_final: 0.9293 (mt) REVERT: B 311 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 328 SER cc_start: 0.9292 (m) cc_final: 0.8831 (t) REVERT: B 336 GLU cc_start: 0.7780 (mp0) cc_final: 0.7502 (mp0) REVERT: B 363 GLU cc_start: 0.8392 (tp30) cc_final: 0.7807 (tm-30) REVERT: B 516 MET cc_start: 0.8253 (mtp) cc_final: 0.7753 (mtm) REVERT: B 541 GLN cc_start: 0.8694 (pm20) cc_final: 0.8425 (pm20) REVERT: C 24 MET cc_start: 0.8721 (mmm) cc_final: 0.8510 (mmm) REVERT: C 26 ASP cc_start: 0.7968 (m-30) cc_final: 0.7740 (m-30) REVERT: C 81 ASN cc_start: 0.8354 (t0) cc_final: 0.8151 (t0) REVERT: C 261 GLU cc_start: 0.8849 (mp0) cc_final: 0.7630 (mp0) REVERT: C 282 MET cc_start: 0.8165 (tpt) cc_final: 0.7624 (tpt) REVERT: C 322 LEU cc_start: 0.9439 (tt) cc_final: 0.9135 (tt) REVERT: C 410 ASP cc_start: 0.8134 (m-30) cc_final: 0.7750 (m-30) REVERT: C 456 GLU cc_start: 0.8666 (pp20) cc_final: 0.8329 (tp30) REVERT: D 154 SER cc_start: 0.9478 (t) cc_final: 0.9205 (p) REVERT: D 197 THR cc_start: 0.8825 (m) cc_final: 0.8349 (p) REVERT: D 200 GLU cc_start: 0.8356 (pt0) cc_final: 0.8125 (pt0) REVERT: D 237 MET cc_start: 0.9131 (mmt) cc_final: 0.8483 (mmm) REVERT: D 338 GLN cc_start: 0.8302 (tt0) cc_final: 0.8010 (tp40) REVERT: D 374 ASP cc_start: 0.7820 (p0) cc_final: 0.7342 (p0) REVERT: D 413 GLN cc_start: 0.8098 (pt0) cc_final: 0.7805 (mt0) REVERT: D 445 MET cc_start: 0.8644 (ttt) cc_final: 0.8408 (ttt) REVERT: E 318 ASP cc_start: 0.8212 (t0) cc_final: 0.7771 (t0) REVERT: E 437 GLN cc_start: 0.8481 (pt0) cc_final: 0.8250 (mm-40) REVERT: E 453 ARG cc_start: 0.7586 (mpt180) cc_final: 0.7340 (mtt90) REVERT: E 461 LYS cc_start: 0.8449 (pttm) cc_final: 0.8042 (pttm) REVERT: F 170 GLN cc_start: 0.7248 (pm20) cc_final: 0.6674 (pp30) REVERT: F 260 MET cc_start: 0.9362 (mmp) cc_final: 0.9137 (mmp) REVERT: F 323 HIS cc_start: 0.8599 (t-90) cc_final: 0.8082 (t-90) REVERT: F 342 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8052 (tp30) REVERT: G 149 LYS cc_start: 0.8738 (tmmt) cc_final: 0.8530 (tmtt) REVERT: G 183 LEU cc_start: 0.9300 (mt) cc_final: 0.9043 (tt) REVERT: H 14 ARG cc_start: 0.8814 (mtt180) cc_final: 0.8090 (mmm-85) REVERT: H 28 GLU cc_start: 0.7881 (pt0) cc_final: 0.7190 (pm20) REVERT: H 60 GLU cc_start: 0.7448 (pp20) cc_final: 0.6450 (mm-30) REVERT: H 89 TYR cc_start: 0.8684 (t80) cc_final: 0.8341 (t80) REVERT: H 90 MET cc_start: 0.8290 (mmm) cc_final: 0.7277 (ttp) outliers start: 1 outliers final: 0 residues processed: 631 average time/residue: 0.2437 time to fit residues: 246.0842 Evaluate side-chains 489 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 285 optimal weight: 4.9990 chunk 471 optimal weight: 50.0000 chunk 451 optimal weight: 50.0000 chunk 110 optimal weight: 0.0470 chunk 219 optimal weight: 20.0000 chunk 454 optimal weight: 40.0000 chunk 236 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 492 optimal weight: 50.0000 chunk 299 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 overall best weight: 6.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN E 170 GLN E 206 GLN E 222 ASN E 262 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087600 restraints weight = 113966.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089373 restraints weight = 75495.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.089899 restraints weight = 49867.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091016 restraints weight = 39750.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.091266 restraints weight = 27230.768| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39027 Z= 0.183 Angle : 0.642 15.524 53230 Z= 0.331 Chirality : 0.044 0.282 6273 Planarity : 0.005 0.062 7224 Dihedral : 5.354 71.219 6204 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.31 (0.12), residues: 5790 helix: 2.12 (0.09), residues: 3184 sheet: -2.09 (0.20), residues: 598 loop : -2.35 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 268 TYR 0.017 0.002 TYR F 383 PHE 0.028 0.002 PHE C 269 TRP 0.024 0.002 TRP F 440 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00408 (39027) covalent geometry : angle 0.64225 (53230) hydrogen bonds : bond 0.03491 ( 2678) hydrogen bonds : angle 4.13402 ( 7950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 677 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7668 (mmp80) cc_final: 0.7288 (mmp80) REVERT: A 102 ILE cc_start: 0.9076 (mt) cc_final: 0.8811 (tt) REVERT: A 282 MET cc_start: 0.8677 (tpt) cc_final: 0.8418 (tpt) REVERT: A 332 GLU cc_start: 0.7972 (pp20) cc_final: 0.5633 (tm-30) REVERT: A 336 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6886 (mm-30) REVERT: A 450 LEU cc_start: 0.8898 (tp) cc_final: 0.7487 (tp) REVERT: A 456 GLU cc_start: 0.8245 (pp20) cc_final: 0.8019 (tm-30) REVERT: A 480 GLU cc_start: 0.8823 (mp0) cc_final: 0.8516 (mp0) REVERT: A 516 MET cc_start: 0.8148 (mtp) cc_final: 0.7810 (ttm) REVERT: A 523 TYR cc_start: 0.8320 (t80) cc_final: 0.7883 (t80) REVERT: B 81 ASN cc_start: 0.8694 (t0) cc_final: 0.8429 (t0) REVERT: B 209 MET cc_start: 0.7812 (ptt) cc_final: 0.7573 (ptt) REVERT: B 311 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 328 SER cc_start: 0.9204 (m) cc_final: 0.8721 (t) REVERT: B 459 GLN cc_start: 0.7555 (mp10) cc_final: 0.7204 (mp10) REVERT: B 478 ASP cc_start: 0.7137 (m-30) cc_final: 0.6745 (p0) REVERT: B 516 MET cc_start: 0.8219 (mtp) cc_final: 0.7843 (mtm) REVERT: B 550 ARG cc_start: 0.7346 (ptt-90) cc_final: 0.7043 (ptt-90) REVERT: C 24 MET cc_start: 0.8756 (mmm) cc_final: 0.8141 (tpt) REVERT: C 261 GLU cc_start: 0.8754 (mp0) cc_final: 0.7750 (mp0) REVERT: C 311 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8122 (tt0) REVERT: C 322 LEU cc_start: 0.9415 (tt) cc_final: 0.9133 (tt) REVERT: C 410 ASP cc_start: 0.8074 (m-30) cc_final: 0.7716 (m-30) REVERT: C 456 GLU cc_start: 0.8659 (pp20) cc_final: 0.8319 (tp30) REVERT: D 154 SER cc_start: 0.9465 (t) cc_final: 0.9237 (p) REVERT: D 197 THR cc_start: 0.8699 (m) cc_final: 0.8431 (p) REVERT: D 237 MET cc_start: 0.9043 (mmt) cc_final: 0.8610 (mmm) REVERT: D 338 GLN cc_start: 0.8284 (tt0) cc_final: 0.7983 (tp40) REVERT: D 374 ASP cc_start: 0.7723 (p0) cc_final: 0.7139 (p0) REVERT: E 316 MET cc_start: 0.7396 (ttm) cc_final: 0.7185 (ttt) REVERT: E 408 ASP cc_start: 0.7999 (m-30) cc_final: 0.7775 (m-30) REVERT: E 424 ASN cc_start: 0.8940 (t0) cc_final: 0.8524 (t0) REVERT: E 437 GLN cc_start: 0.8495 (pt0) cc_final: 0.8162 (mm-40) REVERT: E 461 LYS cc_start: 0.8358 (pttm) cc_final: 0.7982 (pttm) REVERT: F 170 GLN cc_start: 0.7354 (pm20) cc_final: 0.6710 (pp30) REVERT: F 342 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7985 (tp30) REVERT: F 420 ARG cc_start: 0.7555 (mtm110) cc_final: 0.6734 (mtm110) REVERT: G 19 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7709 (ptp-110) REVERT: G 22 GLN cc_start: 0.7806 (tp40) cc_final: 0.7554 (tm-30) REVERT: G 26 ASP cc_start: 0.7901 (t0) cc_final: 0.7634 (t0) REVERT: G 55 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7855 (tm-30) REVERT: G 183 LEU cc_start: 0.9219 (mt) cc_final: 0.8972 (tt) REVERT: H 14 ARG cc_start: 0.8737 (mtt180) cc_final: 0.8042 (mmm-85) REVERT: H 28 GLU cc_start: 0.7788 (pt0) cc_final: 0.7041 (pm20) REVERT: H 57 ARG cc_start: 0.8387 (mpt-90) cc_final: 0.7513 (ptt-90) REVERT: H 60 GLU cc_start: 0.7462 (pp20) cc_final: 0.6405 (mm-30) REVERT: H 89 TYR cc_start: 0.8591 (t80) cc_final: 0.8348 (t80) outliers start: 1 outliers final: 0 residues processed: 678 average time/residue: 0.2534 time to fit residues: 271.6721 Evaluate side-chains 495 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 426 optimal weight: 50.0000 chunk 365 optimal weight: 50.0000 chunk 529 optimal weight: 0.0170 chunk 289 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 408 optimal weight: 30.0000 chunk 381 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 chunk 476 optimal weight: 20.0000 overall best weight: 6.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 222 ASN E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN F 425 GLN G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.112049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087902 restraints weight = 114339.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089210 restraints weight = 71402.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090223 restraints weight = 44770.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090936 restraints weight = 32841.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090734 restraints weight = 30396.572| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39027 Z= 0.192 Angle : 0.650 15.297 53230 Z= 0.337 Chirality : 0.044 0.262 6273 Planarity : 0.005 0.070 7224 Dihedral : 5.251 63.782 6204 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.47 (0.12), residues: 5790 helix: 2.23 (0.09), residues: 3184 sheet: -1.97 (0.21), residues: 593 loop : -2.25 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 420 TYR 0.015 0.002 TYR F 383 PHE 0.037 0.002 PHE D 204 TRP 0.026 0.002 TRP F 440 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00426 (39027) covalent geometry : angle 0.65038 (53230) hydrogen bonds : bond 0.03489 ( 2678) hydrogen bonds : angle 4.08472 ( 7950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9101 (mt) cc_final: 0.8780 (tt) REVERT: A 282 MET cc_start: 0.8600 (tpt) cc_final: 0.8322 (tpt) REVERT: A 283 HIS cc_start: 0.8301 (m170) cc_final: 0.7640 (m-70) REVERT: A 332 GLU cc_start: 0.8065 (pp20) cc_final: 0.5990 (pp20) REVERT: A 336 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 393 GLU cc_start: 0.8242 (mp0) cc_final: 0.7984 (mp0) REVERT: A 456 GLU cc_start: 0.8293 (pp20) cc_final: 0.8063 (tm-30) REVERT: A 480 GLU cc_start: 0.8765 (mp0) cc_final: 0.8527 (mp0) REVERT: A 482 LEU cc_start: 0.9353 (tp) cc_final: 0.9148 (tp) REVERT: A 523 TYR cc_start: 0.8280 (t80) cc_final: 0.7789 (t80) REVERT: B 328 SER cc_start: 0.9251 (m) cc_final: 0.8748 (t) REVERT: B 459 GLN cc_start: 0.7594 (mp10) cc_final: 0.7357 (mp10) REVERT: B 478 ASP cc_start: 0.7385 (m-30) cc_final: 0.6912 (p0) REVERT: B 550 ARG cc_start: 0.7378 (ptt-90) cc_final: 0.7021 (ptt-90) REVERT: C 261 GLU cc_start: 0.8825 (mp0) cc_final: 0.7771 (mp0) REVERT: C 410 ASP cc_start: 0.8038 (m-30) cc_final: 0.7684 (m-30) REVERT: C 456 GLU cc_start: 0.8672 (pp20) cc_final: 0.8344 (tp30) REVERT: D 154 SER cc_start: 0.9481 (t) cc_final: 0.9208 (p) REVERT: D 161 ASN cc_start: 0.8954 (m-40) cc_final: 0.8612 (m110) REVERT: D 237 MET cc_start: 0.8984 (mmt) cc_final: 0.8541 (mmm) REVERT: D 338 GLN cc_start: 0.8263 (tt0) cc_final: 0.7996 (tp40) REVERT: D 374 ASP cc_start: 0.7714 (p0) cc_final: 0.7103 (p0) REVERT: E 245 LEU cc_start: 0.9264 (mm) cc_final: 0.8956 (mt) REVERT: E 316 MET cc_start: 0.7445 (ttm) cc_final: 0.7228 (ttt) REVERT: E 408 ASP cc_start: 0.8077 (m-30) cc_final: 0.7754 (m-30) REVERT: E 424 ASN cc_start: 0.8948 (t0) cc_final: 0.8560 (t0) REVERT: E 437 GLN cc_start: 0.8454 (pt0) cc_final: 0.8129 (mm-40) REVERT: E 461 LYS cc_start: 0.8308 (pttm) cc_final: 0.8007 (pttm) REVERT: F 170 GLN cc_start: 0.7280 (pm20) cc_final: 0.6336 (pp30) REVERT: F 323 HIS cc_start: 0.8517 (t-90) cc_final: 0.8191 (t-90) REVERT: F 334 GLU cc_start: 0.8137 (pt0) cc_final: 0.7901 (mt-10) REVERT: F 342 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7988 (tp30) REVERT: G 26 ASP cc_start: 0.7843 (t0) cc_final: 0.7597 (t0) REVERT: G 153 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7573 (mp0) REVERT: G 183 LEU cc_start: 0.9265 (mt) cc_final: 0.8980 (tt) REVERT: H 14 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8018 (mmm-85) REVERT: H 28 GLU cc_start: 0.7817 (pt0) cc_final: 0.7038 (pm20) REVERT: H 57 ARG cc_start: 0.8309 (mpt-90) cc_final: 0.7356 (ptt-90) REVERT: H 60 GLU cc_start: 0.7413 (pp20) cc_final: 0.6354 (mm-30) REVERT: H 89 TYR cc_start: 0.8684 (t80) cc_final: 0.8433 (t80) REVERT: H 90 MET cc_start: 0.8332 (mmm) cc_final: 0.7272 (ttp) outliers start: 0 outliers final: 0 residues processed: 647 average time/residue: 0.2356 time to fit residues: 244.8395 Evaluate side-chains 500 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 199 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 453 optimal weight: 8.9990 chunk 432 optimal weight: 40.0000 chunk 339 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 412 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 170 GLN E 222 ASN E 310 GLN E 413 GLN E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 3 GLN G 10 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.113850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.089466 restraints weight = 112689.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091138 restraints weight = 71684.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092375 restraints weight = 44415.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092393 restraints weight = 35045.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092765 restraints weight = 28607.303| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39027 Z= 0.143 Angle : 0.618 13.649 53230 Z= 0.319 Chirality : 0.044 0.266 6273 Planarity : 0.004 0.055 7224 Dihedral : 5.035 60.922 6204 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.64 (0.12), residues: 5790 helix: 2.38 (0.09), residues: 3178 sheet: -1.85 (0.21), residues: 589 loop : -2.21 (0.14), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 15 TYR 0.018 0.001 TYR F 288 PHE 0.017 0.001 PHE D 421 TRP 0.023 0.001 TRP F 440 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00320 (39027) covalent geometry : angle 0.61850 (53230) hydrogen bonds : bond 0.03281 ( 2678) hydrogen bonds : angle 3.93947 ( 7950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 664 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9099 (mt) cc_final: 0.8823 (tt) REVERT: A 209 MET cc_start: 0.8330 (ptm) cc_final: 0.8125 (ptm) REVERT: A 282 MET cc_start: 0.8615 (tpt) cc_final: 0.8324 (tpt) REVERT: A 283 HIS cc_start: 0.8193 (m170) cc_final: 0.7549 (m-70) REVERT: A 332 GLU cc_start: 0.8160 (pp20) cc_final: 0.7684 (pp20) REVERT: A 393 GLU cc_start: 0.8144 (mp0) cc_final: 0.7769 (mp0) REVERT: A 480 GLU cc_start: 0.8680 (mp0) cc_final: 0.8329 (mp0) REVERT: B 328 SER cc_start: 0.9197 (m) cc_final: 0.8770 (t) REVERT: B 336 GLU cc_start: 0.7786 (mp0) cc_final: 0.7490 (mp0) REVERT: B 478 ASP cc_start: 0.7239 (m-30) cc_final: 0.6932 (p0) REVERT: B 550 ARG cc_start: 0.7294 (ptt-90) cc_final: 0.6891 (ptt180) REVERT: C 19 MET cc_start: 0.8659 (mmp) cc_final: 0.8456 (mmp) REVERT: C 26 ASP cc_start: 0.7862 (m-30) cc_final: 0.7593 (m-30) REVERT: C 261 GLU cc_start: 0.8701 (mp0) cc_final: 0.7929 (mp0) REVERT: C 300 GLU cc_start: 0.8476 (tp30) cc_final: 0.8161 (mm-30) REVERT: C 410 ASP cc_start: 0.8021 (m-30) cc_final: 0.7714 (m-30) REVERT: C 456 GLU cc_start: 0.8676 (pp20) cc_final: 0.8342 (tp30) REVERT: D 139 ASP cc_start: 0.9191 (m-30) cc_final: 0.8941 (m-30) REVERT: D 154 SER cc_start: 0.9481 (t) cc_final: 0.9242 (p) REVERT: D 237 MET cc_start: 0.9016 (mmt) cc_final: 0.8544 (mmm) REVERT: D 374 ASP cc_start: 0.7687 (p0) cc_final: 0.6990 (p0) REVERT: E 162 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6915 (tm-30) REVERT: E 191 PHE cc_start: 0.9123 (t80) cc_final: 0.8760 (t80) REVERT: E 245 LEU cc_start: 0.9313 (mm) cc_final: 0.9056 (mt) REVERT: E 316 MET cc_start: 0.7350 (ttm) cc_final: 0.7111 (ttt) REVERT: E 408 ASP cc_start: 0.8065 (m-30) cc_final: 0.7761 (m-30) REVERT: E 424 ASN cc_start: 0.8906 (t0) cc_final: 0.8683 (t0) REVERT: E 461 LYS cc_start: 0.8243 (pttm) cc_final: 0.7953 (pttm) REVERT: F 133 THR cc_start: 0.9394 (p) cc_final: 0.8850 (p) REVERT: F 139 ASP cc_start: 0.8628 (m-30) cc_final: 0.7175 (t0) REVERT: F 148 GLN cc_start: 0.8727 (tt0) cc_final: 0.8434 (tt0) REVERT: F 170 GLN cc_start: 0.7268 (pm20) cc_final: 0.6552 (pp30) REVERT: F 260 MET cc_start: 0.9229 (mmm) cc_final: 0.8938 (mmp) REVERT: F 323 HIS cc_start: 0.8539 (t-90) cc_final: 0.7568 (t-170) REVERT: F 342 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7935 (tp30) REVERT: G 19 ARG cc_start: 0.8323 (ttp-110) cc_final: 0.7751 (ptp-110) REVERT: G 31 LYS cc_start: 0.8944 (tttm) cc_final: 0.8678 (tttm) REVERT: G 128 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7732 (ptp-170) REVERT: G 149 LYS cc_start: 0.8280 (tmmt) cc_final: 0.7961 (tmtt) REVERT: G 153 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7609 (mp0) REVERT: G 183 LEU cc_start: 0.9198 (mt) cc_final: 0.8913 (tt) REVERT: H 14 ARG cc_start: 0.8770 (mtt180) cc_final: 0.7977 (mmm-85) REVERT: H 28 GLU cc_start: 0.7849 (pt0) cc_final: 0.7009 (pm20) REVERT: H 57 ARG cc_start: 0.8294 (mpt-90) cc_final: 0.7360 (ptt-90) REVERT: H 60 GLU cc_start: 0.7349 (pp20) cc_final: 0.6410 (mm-30) REVERT: H 90 MET cc_start: 0.8245 (mmm) cc_final: 0.7186 (ttp) outliers start: 0 outliers final: 0 residues processed: 664 average time/residue: 0.2456 time to fit residues: 261.4754 Evaluate side-chains 503 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 56 optimal weight: 7.9990 chunk 334 optimal weight: 4.9990 chunk 223 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 447 optimal weight: 50.0000 chunk 453 optimal weight: 50.0000 chunk 412 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 222 ASN E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN G 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089006 restraints weight = 113122.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090837 restraints weight = 70644.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091428 restraints weight = 43719.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091854 restraints weight = 36244.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091978 restraints weight = 28282.817| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39027 Z= 0.172 Angle : 0.638 14.234 53230 Z= 0.330 Chirality : 0.044 0.281 6273 Planarity : 0.004 0.059 7224 Dihedral : 5.026 52.926 6204 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.73 (0.12), residues: 5790 helix: 2.45 (0.09), residues: 3181 sheet: -1.81 (0.21), residues: 568 loop : -2.16 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 210 TYR 0.021 0.002 TYR F 383 PHE 0.023 0.002 PHE D 421 TRP 0.023 0.002 TRP F 440 HIS 0.005 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00385 (39027) covalent geometry : angle 0.63790 (53230) hydrogen bonds : bond 0.03302 ( 2678) hydrogen bonds : angle 3.92598 ( 7950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.9128 (mt) cc_final: 0.8887 (tt) REVERT: A 283 HIS cc_start: 0.8222 (m170) cc_final: 0.7601 (m-70) REVERT: A 323 MET cc_start: 0.8177 (mmp) cc_final: 0.7976 (mmm) REVERT: A 332 GLU cc_start: 0.8142 (pp20) cc_final: 0.7669 (pp20) REVERT: A 393 GLU cc_start: 0.8172 (mp0) cc_final: 0.7825 (mp0) REVERT: A 480 GLU cc_start: 0.8800 (mp0) cc_final: 0.8431 (mp0) REVERT: B 328 SER cc_start: 0.9222 (m) cc_final: 0.8767 (t) REVERT: B 478 ASP cc_start: 0.7315 (m-30) cc_final: 0.6976 (p0) REVERT: C 19 MET cc_start: 0.8717 (mmp) cc_final: 0.8483 (mmp) REVERT: C 213 ASP cc_start: 0.7973 (t0) cc_final: 0.7244 (t0) REVERT: C 261 GLU cc_start: 0.8726 (mp0) cc_final: 0.7930 (mp0) REVERT: C 410 ASP cc_start: 0.8000 (m-30) cc_final: 0.7723 (m-30) REVERT: C 456 GLU cc_start: 0.8684 (pp20) cc_final: 0.8354 (tp30) REVERT: D 141 MET cc_start: 0.8711 (mtp) cc_final: 0.8382 (mtp) REVERT: D 154 SER cc_start: 0.9395 (t) cc_final: 0.9176 (p) REVERT: D 237 MET cc_start: 0.9026 (mmt) cc_final: 0.8578 (mmm) REVERT: D 413 GLN cc_start: 0.8017 (pt0) cc_final: 0.7750 (mt0) REVERT: E 110 LYS cc_start: 0.8873 (mppt) cc_final: 0.8504 (mmtm) REVERT: E 162 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7297 (tm-30) REVERT: E 244 TYR cc_start: 0.8011 (t80) cc_final: 0.7778 (t80) REVERT: E 245 LEU cc_start: 0.9304 (mm) cc_final: 0.8961 (mt) REVERT: E 316 MET cc_start: 0.7353 (ttm) cc_final: 0.6963 (ttt) REVERT: E 408 ASP cc_start: 0.8092 (m-30) cc_final: 0.7766 (m-30) REVERT: E 424 ASN cc_start: 0.8927 (t0) cc_final: 0.8719 (t0) REVERT: E 461 LYS cc_start: 0.8304 (pttm) cc_final: 0.8050 (pttm) REVERT: F 133 THR cc_start: 0.9419 (p) cc_final: 0.8916 (p) REVERT: F 139 ASP cc_start: 0.8604 (m-30) cc_final: 0.7302 (t0) REVERT: F 170 GLN cc_start: 0.7194 (pm20) cc_final: 0.6690 (pp30) REVERT: F 260 MET cc_start: 0.9251 (mmm) cc_final: 0.8917 (mmp) REVERT: F 323 HIS cc_start: 0.8537 (t-90) cc_final: 0.7631 (t-170) REVERT: F 342 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7909 (tp30) REVERT: G 15 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7435 (mtt90) REVERT: G 128 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7743 (ptp-170) REVERT: G 139 ARG cc_start: 0.9092 (tmm-80) cc_final: 0.8537 (tmm-80) REVERT: G 153 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7650 (mp0) REVERT: G 183 LEU cc_start: 0.9254 (mt) cc_final: 0.8979 (tt) REVERT: H 14 ARG cc_start: 0.8772 (mtt180) cc_final: 0.7946 (mmm-85) REVERT: H 57 ARG cc_start: 0.8317 (mpt-90) cc_final: 0.7380 (ptt-90) REVERT: H 60 GLU cc_start: 0.7245 (pp20) cc_final: 0.6338 (mm-30) REVERT: H 90 MET cc_start: 0.8054 (mmm) cc_final: 0.7391 (ttp) outliers start: 0 outliers final: 0 residues processed: 625 average time/residue: 0.2429 time to fit residues: 244.1324 Evaluate side-chains 495 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 78 optimal weight: 9.9990 chunk 339 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 530 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 40 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 571 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 222 ASN E 375 HIS E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.113552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089438 restraints weight = 113280.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090909 restraints weight = 72651.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091716 restraints weight = 43857.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091925 restraints weight = 33964.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092127 restraints weight = 32252.807| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39027 Z= 0.168 Angle : 0.643 13.993 53230 Z= 0.334 Chirality : 0.045 0.285 6273 Planarity : 0.004 0.064 7224 Dihedral : 5.004 49.572 6204 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.74 (0.12), residues: 5790 helix: 2.44 (0.09), residues: 3189 sheet: -1.77 (0.21), residues: 572 loop : -2.15 (0.14), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 210 TYR 0.022 0.002 TYR F 383 PHE 0.024 0.002 PHE C 269 TRP 0.019 0.002 TRP C 424 HIS 0.006 0.001 HIS C 418 Details of bonding type rmsd covalent geometry : bond 0.00372 (39027) covalent geometry : angle 0.64334 (53230) hydrogen bonds : bond 0.03330 ( 2678) hydrogen bonds : angle 3.92573 ( 7950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.8514 (tpt) cc_final: 0.8260 (tpt) REVERT: A 332 GLU cc_start: 0.8154 (pp20) cc_final: 0.7717 (pp20) REVERT: A 393 GLU cc_start: 0.8204 (mp0) cc_final: 0.7778 (mp0) REVERT: A 480 GLU cc_start: 0.8811 (mp0) cc_final: 0.8416 (mp0) REVERT: B 328 SER cc_start: 0.9178 (m) cc_final: 0.8732 (t) REVERT: B 518 MET cc_start: 0.9031 (mtp) cc_final: 0.8379 (mtm) REVERT: C 24 MET cc_start: 0.9004 (tpt) cc_final: 0.8788 (tpt) REVERT: C 261 GLU cc_start: 0.8710 (mp0) cc_final: 0.7969 (mp0) REVERT: C 287 LEU cc_start: 0.9147 (pp) cc_final: 0.8863 (pp) REVERT: C 410 ASP cc_start: 0.8077 (m-30) cc_final: 0.7800 (m-30) REVERT: C 456 GLU cc_start: 0.8659 (pp20) cc_final: 0.8348 (tp30) REVERT: C 524 LYS cc_start: 0.8559 (pttm) cc_final: 0.8172 (tppt) REVERT: D 141 MET cc_start: 0.8678 (mtp) cc_final: 0.8015 (ttp) REVERT: D 174 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7174 (mtm180) REVERT: D 237 MET cc_start: 0.9014 (mmt) cc_final: 0.8573 (mmm) REVERT: D 413 GLN cc_start: 0.8101 (pt0) cc_final: 0.7771 (mt0) REVERT: D 445 MET cc_start: 0.8528 (ttt) cc_final: 0.8311 (ttt) REVERT: E 58 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7927 (tm-30) REVERT: E 245 LEU cc_start: 0.9314 (mm) cc_final: 0.8962 (mt) REVERT: E 316 MET cc_start: 0.7317 (ttm) cc_final: 0.6847 (ttt) REVERT: E 408 ASP cc_start: 0.8118 (m-30) cc_final: 0.7783 (m-30) REVERT: E 461 LYS cc_start: 0.8307 (pttm) cc_final: 0.8060 (pttm) REVERT: F 7 GLU cc_start: 0.7204 (mp0) cc_final: 0.6739 (mp0) REVERT: F 133 THR cc_start: 0.9434 (p) cc_final: 0.8842 (p) REVERT: F 139 ASP cc_start: 0.8628 (m-30) cc_final: 0.7334 (t0) REVERT: F 170 GLN cc_start: 0.7236 (pm20) cc_final: 0.6760 (pp30) REVERT: F 260 MET cc_start: 0.9254 (mmm) cc_final: 0.8921 (mmp) REVERT: F 342 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7850 (tp30) REVERT: G 31 LYS cc_start: 0.8962 (tttm) cc_final: 0.8761 (tttm) REVERT: G 128 ARG cc_start: 0.8324 (mmt90) cc_final: 0.7919 (ptp-170) REVERT: G 139 ARG cc_start: 0.9073 (tmm-80) cc_final: 0.8554 (tmm-80) REVERT: G 183 LEU cc_start: 0.9236 (mt) cc_final: 0.8973 (tt) REVERT: H 1 MET cc_start: 0.7492 (mmm) cc_final: 0.6921 (mmt) REVERT: H 14 ARG cc_start: 0.8774 (mtt180) cc_final: 0.7943 (mmm-85) REVERT: H 57 ARG cc_start: 0.8316 (mpt-90) cc_final: 0.7480 (ptt-90) REVERT: H 90 MET cc_start: 0.8083 (mmm) cc_final: 0.7404 (ttp) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.2367 time to fit residues: 239.5863 Evaluate side-chains 479 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 354 optimal weight: 40.0000 chunk 227 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 399 optimal weight: 40.0000 chunk 60 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 357 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 323 optimal weight: 20.0000 chunk 508 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 222 ASN E 249 HIS E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.112917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088617 restraints weight = 113484.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090322 restraints weight = 72073.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091127 restraints weight = 42339.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091254 restraints weight = 36053.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091677 restraints weight = 31033.416| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39027 Z= 0.192 Angle : 0.669 14.612 53230 Z= 0.347 Chirality : 0.046 0.295 6273 Planarity : 0.005 0.059 7224 Dihedral : 5.037 48.190 6204 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.75 (0.12), residues: 5790 helix: 2.45 (0.09), residues: 3189 sheet: -1.83 (0.21), residues: 567 loop : -2.14 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 154 TYR 0.026 0.002 TYR E 244 PHE 0.022 0.002 PHE C 269 TRP 0.025 0.002 TRP F 440 HIS 0.009 0.001 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00432 (39027) covalent geometry : angle 0.66891 (53230) hydrogen bonds : bond 0.03375 ( 2678) hydrogen bonds : angle 3.97117 ( 7950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11580 Ramachandran restraints generated. 5790 Oldfield, 0 Emsley, 5790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 MET cc_start: 0.8509 (tpt) cc_final: 0.8237 (tpt) REVERT: A 323 MET cc_start: 0.8223 (mmp) cc_final: 0.7922 (mmm) REVERT: A 332 GLU cc_start: 0.8177 (pp20) cc_final: 0.7735 (pp20) REVERT: A 393 GLU cc_start: 0.8273 (mp0) cc_final: 0.7847 (mp0) REVERT: A 480 GLU cc_start: 0.8804 (mp0) cc_final: 0.8434 (mp0) REVERT: B 292 SER cc_start: 0.9339 (m) cc_final: 0.8887 (p) REVERT: B 328 SER cc_start: 0.9204 (m) cc_final: 0.8769 (t) REVERT: B 391 MET cc_start: 0.6790 (mmt) cc_final: 0.6404 (mmp) REVERT: B 449 GLU cc_start: 0.8742 (mp0) cc_final: 0.8536 (mp0) REVERT: B 518 MET cc_start: 0.9041 (mtp) cc_final: 0.8378 (mtm) REVERT: C 24 MET cc_start: 0.9016 (tpt) cc_final: 0.8616 (tmm) REVERT: C 261 GLU cc_start: 0.8772 (mp0) cc_final: 0.7972 (mp0) REVERT: C 264 ASP cc_start: 0.8318 (t0) cc_final: 0.7526 (t0) REVERT: C 410 ASP cc_start: 0.8028 (m-30) cc_final: 0.7753 (m-30) REVERT: C 456 GLU cc_start: 0.8656 (pp20) cc_final: 0.8346 (tp30) REVERT: C 524 LYS cc_start: 0.8558 (pttm) cc_final: 0.8175 (tppt) REVERT: D 141 MET cc_start: 0.8317 (mtp) cc_final: 0.8006 (ttp) REVERT: D 237 MET cc_start: 0.9023 (mmt) cc_final: 0.8578 (mmm) REVERT: D 413 GLN cc_start: 0.8004 (pt0) cc_final: 0.7681 (mt0) REVERT: D 445 MET cc_start: 0.8576 (ttt) cc_final: 0.8343 (ttt) REVERT: E 58 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8120 (tm-30) REVERT: E 245 LEU cc_start: 0.9265 (mm) cc_final: 0.8991 (mt) REVERT: E 316 MET cc_start: 0.7473 (ttm) cc_final: 0.7131 (ttt) REVERT: E 325 ILE cc_start: 0.8969 (mm) cc_final: 0.8288 (mm) REVERT: E 408 ASP cc_start: 0.8098 (m-30) cc_final: 0.7799 (m-30) REVERT: F 133 THR cc_start: 0.9434 (p) cc_final: 0.8859 (p) REVERT: F 139 ASP cc_start: 0.8642 (m-30) cc_final: 0.7642 (t0) REVERT: F 170 GLN cc_start: 0.7251 (pm20) cc_final: 0.6796 (pp30) REVERT: F 260 MET cc_start: 0.9253 (mmm) cc_final: 0.8964 (mmp) REVERT: F 281 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7828 (ptp-170) REVERT: F 316 MET cc_start: 0.8592 (mpp) cc_final: 0.8289 (mpp) REVERT: F 323 HIS cc_start: 0.8206 (t-90) cc_final: 0.7578 (t-90) REVERT: F 342 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7862 (tp30) REVERT: G 15 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7400 (mtt90) REVERT: G 31 LYS cc_start: 0.8981 (tttm) cc_final: 0.8749 (tttm) REVERT: G 128 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7877 (ptp-170) REVERT: G 139 ARG cc_start: 0.9110 (tmm-80) cc_final: 0.8579 (tmm-80) REVERT: G 183 LEU cc_start: 0.9243 (mt) cc_final: 0.8982 (tt) REVERT: H 14 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7921 (mmm-85) REVERT: H 90 MET cc_start: 0.8061 (mmm) cc_final: 0.7470 (ttp) REVERT: H 96 LYS cc_start: 0.9200 (ptmm) cc_final: 0.8740 (mmmt) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.2395 time to fit residues: 235.9302 Evaluate side-chains 472 residues out of total 4575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 257 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 346 optimal weight: 50.0000 chunk 26 optimal weight: 5.9990 chunk 570 optimal weight: 40.0000 chunk 308 optimal weight: 9.9990 chunk 558 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 142 ASN E 428 GLN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 428 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088130 restraints weight = 114050.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089559 restraints weight = 73704.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090557 restraints weight = 45416.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090852 restraints weight = 35082.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091123 restraints weight = 29069.694| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 39027 Z= 0.208 Angle : 0.682 15.211 53230 Z= 0.354 Chirality : 0.046 0.297 6273 Planarity : 0.005 0.057 7224 Dihedral : 5.088 47.462 6204 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.73 (0.12), residues: 5790 helix: 2.44 (0.09), residues: 3195 sheet: -1.90 (0.21), residues: 574 loop : -2.14 (0.14), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 210 TYR 0.028 0.002 TYR F 383 PHE 0.024 0.002 PHE B 563 TRP 0.019 0.002 TRP C 424 HIS 0.010 0.002 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00467 (39027) covalent geometry : angle 0.68241 (53230) hydrogen bonds : bond 0.03435 ( 2678) hydrogen bonds : angle 3.99641 ( 7950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6481.40 seconds wall clock time: 112 minutes 11.58 seconds (6731.58 seconds total)